Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses id...
Saved in:
| Published in | Cell Vol. 179; no. 4; pp. 964 - 983.e31 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
31.10.2019
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2019.10.007 |
Cover
| Abstract | To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.
[Display omitted]
•Integrated proteogenomic characterization in 103 ccRCC cases•Delineation of chromosomal translocation events leading to chromosome 3p loss•Tumor-specific proteomic/phosphoproteomic alterations unrevealed by mRNA analysis•Immune-based subtypes of ccRCC defined by mRNA, proteome, and phosphoproteome
Comprehensive proteogenomic characterization in 103 treatment-naive clear cell renal cell carcinoma patient samples highlights tumor-specific alterations at the proteomic level that are unrevealed by transcriptomic profiling and proposes a revised subtyping scheme based on integrated omics analysis. |
|---|---|
| AbstractList | To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.
[Display omitted]
•Integrated proteogenomic characterization in 103 ccRCC cases•Delineation of chromosomal translocation events leading to chromosome 3p loss•Tumor-specific proteomic/phosphoproteomic alterations unrevealed by mRNA analysis•Immune-based subtypes of ccRCC defined by mRNA, proteome, and phosphoproteome
Comprehensive proteogenomic characterization in 103 treatment-naive clear cell renal cell carcinoma patient samples highlights tumor-specific alterations at the proteomic level that are unrevealed by transcriptomic profiling and proposes a revised subtyping scheme based on integrated omics analysis. To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology. To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology. To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology. To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology. Comprehensive proteogenomic characterization in 103 treatment-naive clear cell renal cell carcinoma patient samples highlights tumor-specific alterations at the proteomic level that are unrevealed by transcriptomic profiling and proposes a revised subtyping scheme based on integrated omics analysis. |
| Author | Skelly, Tara Shi, Zhiao Chheda, Milan G. Hu, Yingwei Richey, Shannon Robles, Ana I. Elburn, Kim Castro, Patricia Ma, Shiyong Kong, Andy Rykunov, Dmitry Birger, Chet Smith, Richard D. Valley, Dana R. Ittmann, Michael M. Holloway, Kimberly Sokoll, Lori J. Zhang, Bing Tansil, Darlene Zhang, Zhen Vatanian, Negin Vasaikar, Suhas Li, Qing Kay Zhou, Daniel C. Chinnaiyan, Arul M. Velvulou, Uma Clark, David J. Modugno, Francesmary Tyner, Jeffrey W. Li, Kai Antczak, Andrzej McGee, John Hakimi, A. Ari Geiszler, Daniel Rodriguez, Henry Chan, Daniel W. Avtonomov, Dmitry M. Kim, Beom-Jun Eschbacher, Jennifer Cottingham, Sandra Hoadley, Katherine A. Sengupta, Sohini Wang, Liang-Bo Lubinski, Jan Petralia, Francesca Hariharan, Pushpa Smith, Michael Qi, Liqun Boca, Simina M. Perou, Amy M. Wang, Pei Wheeler, David Demir, Emek Mani, D.R. Reva, Boris Hiltke, Tara Lewis, Michael Omelchenko, Tatiana Westbrook, Thomas Cao, Song Cai, Shuang Petyuk, Vladislav A. Tognon, Cristina Wen, Bo Hilsenbeck, Sue Edwards, Nathan J. Teo, Guo Ci Hong, Runyu Liu, Hongwei Kalayci, Selim Mareedu |
| AuthorAffiliation | 27 Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA 28 Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA 31 Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA 2 Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA 23 Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 71-252, Poland 32 These authors contributed equally 6 Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA 20 Department of Urology, Poznań University of Medical Sciences, Szwajcarska 3, Poznań 61-285, Poland 19 Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA 15 Departments of Medicine and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA 4 Department of Population Health Science and Policy, Icahn School of Medicine at Mo |
| AuthorAffiliation_xml | – name: 4 Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – name: 17 Brady Urological Institute and Department of Urology, Johns Hopkins University, Baltimore, MD 21231, USA – name: 7 Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA – name: 30 Sema4, Stamford, CT 06902, USA – name: 26 Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA – name: 12 Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA – name: 20 Department of Urology, Poznań University of Medical Sciences, Szwajcarska 3, Poznań 61-285, Poland – name: 11 Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA – name: 15 Departments of Medicine and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA – name: 18 Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA – name: 1 Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – name: 16 Department of Biochemistry and Cellular Biology, Georgetown University, Washington, DC 20007, USA – name: 6 Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA – name: 29 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA – name: 34 Lead Contact – name: 19 Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA – name: 8 Washington University School of Medicine, St. Louis, MO 63110, USA – name: 14 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA – name: 28 Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA – name: 32 These authors contributed equally – name: 27 Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA – name: 2 Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA – name: 13 Department of Medicine, New York University School of Medicine, New York, NY 10016, USA – name: 21 Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA – name: 33 These authors contributed equally – name: 3 Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – name: 31 Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA – name: 5 Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – name: 24 International Institute for Molecular Oncology, Poznań 60-203, Poland – name: 9 Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA – name: 23 Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 71-252, Poland – name: 10 Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA – name: 25 Poznań University of Medical Sciences, Poznan 60-701, Poland – name: 22 Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA |
| Author_xml | – sequence: 4 givenname: Jianbo surname: Pan fullname: Pan, Jianbo organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 6 givenname: Yingwei surname: Hu fullname: Hu, Yingwei organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 15 givenname: Azra surname: Krek fullname: Krek, Azra organization: Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – sequence: 16 givenname: Yize surname: Li fullname: Li, Yize organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 19 givenname: Lin S. surname: Chen fullname: Chen, Lin S. organization: Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA – sequence: 21 givenname: Suhas surname: Vasaikar fullname: Vasaikar, Suhas organization: Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA – sequence: 22 givenname: Yige surname: Wu fullname: Wu, Yige organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 24 givenname: Shrabanti surname: Chowdhury fullname: Chowdhury, Shrabanti organization: Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – sequence: 25 givenname: Matthew A. surname: Wyczalkowski fullname: Wyczalkowski, Matthew A. organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 28 givenname: Andy surname: Kong fullname: Kong, Andy organization: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 29 givenname: Sunantha surname: Sethuraman fullname: Sethuraman, Sunantha organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 30 givenname: Dmitry M. surname: Avtonomov fullname: Avtonomov, Dmitry M. organization: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 32 givenname: Antonio surname: Colaprico fullname: Colaprico, Antonio organization: Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA – sequence: 33 givenname: Song surname: Cao fullname: Cao, Song organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 34 givenname: Kyung-Cho surname: Cho fullname: Cho, Kyung-Cho organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 35 givenname: Selim surname: Kalayci fullname: Kalayci, Selim organization: Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA – sequence: 36 givenname: Shiyong surname: Ma fullname: Ma, Shiyong organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 38 givenname: Kelly surname: Ruggles fullname: Ruggles, Kelly organization: Department of Medicine, New York University School of Medicine, New York, NY 10016, USA – sequence: 42 givenname: Emily surname: Kawaler fullname: Kawaler, Emily organization: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA – sequence: 44 givenname: Bo surname: Wen fullname: Wen, Bo organization: Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA – sequence: 48 givenname: Feng surname: Chen fullname: Chen, Feng organization: Departments of Medicine and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 49 givenname: Nathan surname: Edwards fullname: Edwards, Nathan organization: Department of Biochemistry and Cellular Biology, Georgetown University, Washington, DC 20007, USA – sequence: 50 givenname: Phillip M. surname: Pierorazio fullname: Pierorazio, Phillip M. organization: Brady Urological Institute and Department of Urology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 52 givenname: Christian P. surname: Pavlovich fullname: Pavlovich, Christian P. organization: Brady Urological Institute and Department of Urology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 54 givenname: Gabriel surname: Brominski fullname: Brominski, Gabriel organization: Department of Urology, Poznań University of Medical Sciences, Szwajcarska 3, Poznań 61-285, Poland – sequence: 55 givenname: James J. surname: Hsieh fullname: Hsieh, James J. organization: Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 58 givenname: Jan surname: Lubinski fullname: Lubinski, Jan organization: Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 71-252, Poland – sequence: 59 givenname: Maciej surname: Wiznerowicz fullname: Wiznerowicz, Maciej organization: International Institute for Molecular Oncology, Poznań 60-203, Poland – sequence: 61 givenname: Christopher R. surname: Kinsinger fullname: Kinsinger, Christopher R. organization: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA – sequence: 62 givenname: Mathangi surname: Thiagarajan fullname: Thiagarajan, Mathangi organization: Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA – sequence: 64 givenname: Mehdi surname: Mesri fullname: Mesri, Mehdi organization: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA – sequence: 65 givenname: Tara surname: Hiltke fullname: Hiltke, Tara organization: Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA – sequence: 71 givenname: Li surname: Ding fullname: Ding, Li organization: Washington University School of Medicine, St. Louis, MO 63110, USA – sequence: 74 givenname: Zhen surname: Zhang fullname: Zhang, Zhen organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 75 givenname: Gilbert S. surname: Omenn fullname: Omenn, Gilbert S. organization: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 76 givenname: Marcin surname: Cieslik fullname: Cieslik, Marcin email: mcieslik@med.mich.edu organization: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 78 givenname: Alexey I. surname: Nesvizhskii fullname: Nesvizhskii, Alexey I. email: nesvi@med.umich.edu organization: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 80 givenname: Hui surname: Zhang fullname: Zhang, Hui email: huizhang@jhu.edu organization: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA – sequence: 81 givenname: Abdul Samad surname: Hashimi fullname: Hashimi, Abdul Samad – sequence: 84 givenname: Alyssa surname: Charamut fullname: Charamut, Alyssa – sequence: 93 givenname: Brian J. surname: Druker fullname: Druker, Brian J. – sequence: 97 givenname: Cristina surname: Tognon fullname: Tognon, Cristina – sequence: 98 givenname: D.R. surname: Mani fullname: Mani, D.R. – sequence: 100 givenname: Daniel C. surname: Rohrer fullname: Rohrer, Daniel C. – sequence: 102 givenname: Darlene surname: Tansil fullname: Tansil, Darlene – sequence: 103 givenname: David surname: Chesla fullname: Chesla, David – sequence: 104 givenname: David surname: Heiman fullname: Heiman, David – sequence: 105 givenname: David surname: Wheeler fullname: Wheeler, David – sequence: 107 givenname: Doug surname: Chan fullname: Chan, Doug – sequence: 108 givenname: Emek surname: Demir fullname: Demir, Emek – sequence: 113 givenname: George D. surname: Wilson fullname: Wilson, George D. – sequence: 116 givenname: Hongwei surname: Liu fullname: Liu, Hongwei – sequence: 119 givenname: Hua surname: Zhou fullname: Zhou, Hua – sequence: 120 givenname: Jacob surname: Day fullname: Day, Jacob – sequence: 121 givenname: James surname: Suh fullname: Suh, James – sequence: 124 givenname: Jeffrey R. surname: Whiteaker fullname: Whiteaker, Jeffrey R. – sequence: 126 givenname: Jennifer surname: Eschbacher fullname: Eschbacher, Jennifer – sequence: 127 givenname: Jin surname: Chen fullname: Chen, Jin – sequence: 130 givenname: Karen A. surname: Ketchum fullname: Ketchum, Karen A. – sequence: 131 givenname: Karin D. surname: Rodland fullname: Rodland, Karin D. – sequence: 134 givenname: Karsten surname: Krug fullname: Krug, Karsten – sequence: 138 givenname: Kimberly surname: Holloway fullname: Holloway, Kimberly – sequence: 143 givenname: Lori J. surname: Sokoll fullname: Sokoll, Lori J. – sequence: 144 givenname: MacIntosh surname: Cornwell fullname: Cornwell, MacIntosh – sequence: 145 givenname: Marc surname: Loriaux fullname: Loriaux, Marc – sequence: 148 givenname: Matthew surname: Anderson fullname: Anderson, Matthew – sequence: 150 givenname: Matthew J. surname: Ellis fullname: Ellis, Matthew J. – sequence: 151 givenname: Maureen surname: Dyer fullname: Dyer, Maureen – sequence: 153 givenname: Meghan C. surname: Burke fullname: Burke, Meghan C. – sequence: 154 givenname: Melissa surname: Borucki fullname: Borucki, Melissa – sequence: 155 givenname: Michael A. surname: Gillette fullname: Gillette, Michael A. – sequence: 156 givenname: Michael J. surname: Birrer fullname: Birrer, Michael J. – sequence: 159 givenname: Michael surname: Smith fullname: Smith, Michael – sequence: 163 givenname: Munziba surname: Khan fullname: Khan, Munziba – sequence: 164 givenname: Nancy surname: Roche fullname: Roche, Nancy – sequence: 165 givenname: Nathan J. surname: Edwards fullname: Edwards, Nathan J. – sequence: 166 givenname: Negin surname: Vatanian fullname: Vatanian, Negin – sequence: 167 givenname: Nicole surname: Tignor fullname: Tignor, Nicole – sequence: 171 givenname: Paul surname: Piehowski fullname: Piehowski, Paul – sequence: 172 givenname: Peter B. surname: McGarvey fullname: McGarvey, Peter B. – sequence: 174 givenname: Pushpa surname: Hariharan fullname: Hariharan, Pushpa – sequence: 175 givenname: Qingsong surname: Gao fullname: Gao, Qingsong – sequence: 178 givenname: Ratna R. surname: Thangudu fullname: Thangudu, Ratna R. – sequence: 179 givenname: Rebecca surname: Montgomery fullname: Montgomery, Rebecca – sequence: 184 givenname: Ross surname: Bremner fullname: Bremner, Ross – sequence: 185 givenname: Ruiyang surname: Liu fullname: Liu, Ruiyang – sequence: 186 givenname: Runyu surname: Hong fullname: Hong, Runyu – sequence: 188 givenname: Samuel H. surname: Payne fullname: Payne, Samuel H. – sequence: 192 givenname: Shalin surname: Patel fullname: Patel, Shalin – sequence: 193 givenname: Shankha surname: Satpathy fullname: Satpathy, Shankha – sequence: 195 givenname: Sherri R. surname: Davies fullname: Davies, Sherri R. – sequence: 198 givenname: Snehal surname: Patil fullname: Patil, Snehal – sequence: 200 givenname: Sonya surname: Carter fullname: Carter, Sonya – sequence: 201 givenname: Stacey surname: Gabriel fullname: Gabriel, Stacey – sequence: 202 givenname: Stefani N. surname: Thomas fullname: Thomas, Stefani N. – sequence: 205 givenname: Steven A. surname: Carr fullname: Carr, Steven A. – sequence: 210 givenname: Tara surname: Skelly fullname: Skelly, Tara – sequence: 212 givenname: Uma surname: Borate fullname: Borate, Uma – sequence: 221 givenname: Yosef surname: Maruvka fullname: Maruvka, Yosef – sequence: 222 givenname: Zhi surname: Li fullname: Li, Zhi |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31675502$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNUV1rFDEUDVKx2-of8EHm0ZdZb74mMyCCDFoLC4roc8hkbrZZZpOayRbqrzfTbUV9KD4l3HvOuYdzzshJiAEJeUlhTYE2b3Zri9O0ZkC7MlgDqCdkRaFTtaCKnZAVQMfqtlHilJzN8w4AWinlM3LKaaOkBLYim8uQcZtMxrH6kmLGuMUQ995W_ZVJxmZM_qfJPoYquqqf0KSqL1errxjMdPz2JllfSOY5eerMNOOL-_ecfP_44Vv_qd58vrjs329qK6XItXMdSCekHWBsOmdBtMOghGPSOMEHxx2gdE4ZQQEkb8E448aBMdYqyQfKz8m7o-71YdjjaDHkZCZ9nfzepFsdjdd_b4K_0tt4oxXnJR9eBF7fC6T444Bz1ns_L2GagPEwa8aVoJ0oMf4HlNJGNi0XBfrqT1u__TykXQDtEWBTnOeETluf78ItLv2kKeilWL3TywG9FLvMSrGFyv6hPqg_Snp7JGEp48Zj0rP1GCyOPqHNeoz-MfovVDa82g |
| CitedBy_id | crossref_primary_10_3390_jpm14121157 crossref_primary_10_1002_pmic_202000043 crossref_primary_10_1016_j_xcrm_2025_101989 crossref_primary_10_1038_s41467_024_46132_y crossref_primary_10_3389_fimmu_2023_1276658 crossref_primary_10_1038_s41598_024_62978_0 crossref_primary_10_1016_j_isci_2022_103798 crossref_primary_10_1080_10799893_2021_1883060 crossref_primary_10_1016_j_ccell_2020_12_007 crossref_primary_10_3390_ijms24119629 crossref_primary_10_1016_j_xcrm_2020_100004 crossref_primary_10_1002_pmic_202000161 crossref_primary_10_1007_s10238_023_01274_z crossref_primary_10_1093_bioinformatics_btab612 crossref_primary_10_1186_s12967_023_03978_y crossref_primary_10_1038_s41418_024_01378_3 crossref_primary_10_3390_biomedicines10112953 crossref_primary_10_1038_s41581_020_00359_2 crossref_primary_10_1002_mas_21827 crossref_primary_10_1093_pcmedi_pbad019 crossref_primary_10_3389_fonc_2022_814120 crossref_primary_10_1038_s41435_024_00312_4 crossref_primary_10_1038_s41592_023_02120_6 crossref_primary_10_1021_acs_analchem_3c01497 crossref_primary_10_1016_j_eururo_2022_06_016 crossref_primary_10_1007_s12672_024_00930_4 crossref_primary_10_1002_advs_202203718 crossref_primary_10_1016_j_bioorg_2023_106454 crossref_primary_10_3390_ijms25147639 crossref_primary_10_1002_1878_0261_13625 crossref_primary_10_1016_j_esmoop_2025_104294 crossref_primary_10_1002_pmic_202300242 crossref_primary_10_3389_fgene_2022_873884 crossref_primary_10_1016_j_eururo_2022_07_032 crossref_primary_10_1080_14789450_2021_1976152 crossref_primary_10_1002_advs_202404033 crossref_primary_10_1007_s00345_021_03786_3 crossref_primary_10_1200_PO_23_00565 crossref_primary_10_3389_fonc_2022_1012138 crossref_primary_10_3389_fgene_2023_1071694 crossref_primary_10_1021_acs_jproteome_0c00380 crossref_primary_10_1186_s12885_021_09033_7 crossref_primary_10_1016_j_xcrm_2024_101547 crossref_primary_10_1038_s41422_022_00736_5 crossref_primary_10_3390_cancers15235530 crossref_primary_10_1038_s41598_023_39809_9 crossref_primary_10_1038_s41586_022_05333_5 crossref_primary_10_1093_pcmedi_pbac028 crossref_primary_10_1021_acs_jproteome_9b00745 crossref_primary_10_3390_ijms22126290 crossref_primary_10_1093_bib_bbab212 crossref_primary_10_1182_blood_2022016033 crossref_primary_10_3389_fphar_2022_927299 crossref_primary_10_1155_2021_7190301 crossref_primary_10_3389_fonc_2021_751430 crossref_primary_10_1186_s40164_024_00548_w crossref_primary_10_1093_nar_gkad841 crossref_primary_10_1093_jmcb_mjab031 crossref_primary_10_2147_IJGM_S341801 crossref_primary_10_3390_cancers16162844 crossref_primary_10_1002_pmic_202000136 crossref_primary_10_1074_mcp_TIR120_002216 crossref_primary_10_1007_s12032_021_01554_2 crossref_primary_10_1111_cas_16206 crossref_primary_10_1016_j_molcel_2021_03_028 crossref_primary_10_1016_j_jpha_2023_08_021 crossref_primary_10_1021_acs_jproteome_0c00485 crossref_primary_10_1021_acs_jproteome_4c00558 crossref_primary_10_1016_j_humpath_2022_07_022 crossref_primary_10_1021_acs_jproteome_4c00431 crossref_primary_10_5306_wjco_v11_i9_679 crossref_primary_10_1038_s41591_023_02790_x crossref_primary_10_1093_function_zqae012 crossref_primary_10_3389_fonc_2021_621278 crossref_primary_10_1172_jci_insight_171916 crossref_primary_10_1016_j_semcancer_2020_10_015 crossref_primary_10_1038_s41467_019_13528_0 crossref_primary_10_7554_eLife_75227 crossref_primary_10_1007_s00432_023_05349_y crossref_primary_10_3390_cimb46120817 crossref_primary_10_1038_s41598_021_94019_5 crossref_primary_10_1016_j_labinv_2025_104130 crossref_primary_10_1159_000512446 crossref_primary_10_1016_j_celrep_2021_110055 crossref_primary_10_1093_nar_gkad824 crossref_primary_10_1016_j_clgc_2024_102266 crossref_primary_10_1073_pnas_2103240118 crossref_primary_10_1111_cas_16228 crossref_primary_10_1021_acs_analchem_3c05785 crossref_primary_10_3389_fonc_2024_1446324 crossref_primary_10_1158_2159_8290_CD_22_0236 crossref_primary_10_1016_j_canlet_2020_05_034 crossref_primary_10_1093_jmcb_mjaa033 crossref_primary_10_1016_j_phrs_2023_106844 crossref_primary_10_1155_2022_4673514 crossref_primary_10_1038_s41467_024_44911_1 crossref_primary_10_3390_biomedicines11041010 crossref_primary_10_1038_s41467_024_52285_7 crossref_primary_10_1038_s41585_022_00676_0 crossref_primary_10_1016_j_urolonc_2021_12_005 crossref_primary_10_1016_j_mcpro_2021_100123 crossref_primary_10_1038_s41581_019_0233_5 crossref_primary_10_1038_s42003_021_02636_7 crossref_primary_10_3389_fonc_2022_780631 crossref_primary_10_1177_17588359211059367 crossref_primary_10_1038_s41467_023_39981_6 crossref_primary_10_2174_1570164620666230328120621 crossref_primary_10_1038_s41419_020_03268_1 crossref_primary_10_1038_s41388_024_03007_2 crossref_primary_10_1186_s12014_022_09373_x crossref_primary_10_18632_aging_205300 crossref_primary_10_1093_nar_gkaa498 crossref_primary_10_1016_j_mcpro_2022_100417 crossref_primary_10_1016_j_neucom_2021_11_094 crossref_primary_10_1155_2024_3468209 crossref_primary_10_1002_pmic_201900344 crossref_primary_10_1016_j_jprot_2022_104808 crossref_primary_10_1002_mef2_36 crossref_primary_10_3390_cancers14225607 crossref_primary_10_2174_1381612829666230316110932 crossref_primary_10_3390_cancers15092500 crossref_primary_10_1016_j_ccell_2023_12_015 crossref_primary_10_1016_j_jprot_2022_104810 crossref_primary_10_1186_s12935_021_02046_z crossref_primary_10_1016_j_pathol_2024_05_012 crossref_primary_10_1016_j_celrep_2023_112409 crossref_primary_10_1002_pmic_201900358 crossref_primary_10_1021_acs_jproteome_3c00186 crossref_primary_10_1177_17588359231197957 crossref_primary_10_1039_D0MO00188K crossref_primary_10_3390_cancers15245797 crossref_primary_10_3390_cimb45120594 crossref_primary_10_1016_j_bbcan_2024_189240 crossref_primary_10_1002_pmic_201900359 crossref_primary_10_1021_acsomega_4c07398 crossref_primary_10_1021_acs_jproteome_4c00586 crossref_primary_10_1016_j_xcrm_2023_101358 crossref_primary_10_1016_j_biocel_2023_106383 crossref_primary_10_1016_j_path_2022_07_005 crossref_primary_10_1016_j_xcrm_2023_101359 crossref_primary_10_3389_fimmu_2022_956679 crossref_primary_10_1038_s41467_023_41139_3 crossref_primary_10_1016_j_cels_2023_07_007 crossref_primary_10_1038_s41467_023_37221_5 crossref_primary_10_1021_acs_jproteome_3c00196 crossref_primary_10_1016_j_cell_2021_08_023 crossref_primary_10_1002_advs_202401041 crossref_primary_10_1093_nsr_nwad167 crossref_primary_10_1016_j_biomaterials_2022_121488 crossref_primary_10_1016_j_csbj_2024_04_044 crossref_primary_10_1016_j_csbj_2022_09_019 crossref_primary_10_1021_acs_jproteome_4c00294 crossref_primary_10_1038_s41467_020_17641_3 crossref_primary_10_1158_2159_8290_CD_21_0211 crossref_primary_10_1016_j_isci_2025_112198 crossref_primary_10_3389_fimmu_2022_830220 crossref_primary_10_1089_nsm_2019_0010 crossref_primary_10_1038_s43018_021_00250_4 crossref_primary_10_1002_pmic_202400271 crossref_primary_10_1016_j_esmoop_2023_101642 crossref_primary_10_3389_fonc_2020_01770 crossref_primary_10_26508_lsa_202201680 crossref_primary_10_1080_15384047_2024_2345977 crossref_primary_10_3390_diagnostics12102452 crossref_primary_10_3390_medicines7080044 crossref_primary_10_1038_s41467_022_29577_x crossref_primary_10_1021_acs_jproteome_3c00491 crossref_primary_10_1016_j_tranon_2020_100974 crossref_primary_10_3390_cancers14041095 crossref_primary_10_1016_j_cels_2024_01_009 crossref_primary_10_1038_s41467_022_35036_4 crossref_primary_10_1186_s13073_024_01415_3 crossref_primary_10_1016_j_ccell_2021_01_006 crossref_primary_10_1155_2022_2124088 crossref_primary_10_1016_j_ejmech_2024_116209 crossref_primary_10_1089_dna_2020_5601 crossref_primary_10_1038_s41467_022_30342_3 crossref_primary_10_1002_tox_24319 crossref_primary_10_1038_s41467_022_33385_8 crossref_primary_10_1038_s41467_023_39828_0 crossref_primary_10_3390_ijms21030829 crossref_primary_10_2139_ssrn_3922641 crossref_primary_10_3389_fcell_2021_659294 crossref_primary_10_1021_acs_analchem_9b04474 crossref_primary_10_1016_j_isci_2023_108367 crossref_primary_10_1016_j_xcrm_2023_101173 crossref_primary_10_3390_cells11030472 crossref_primary_10_3390_genes15050621 crossref_primary_10_1002_cam4_4311 crossref_primary_10_1021_acs_jproteome_3c00155 crossref_primary_10_1186_s40001_024_01763_1 crossref_primary_10_1038_s41467_023_37440_w crossref_primary_10_1186_s12014_023_09437_6 crossref_primary_10_1016_j_isci_2023_108370 crossref_primary_10_3233_KCA_200085 crossref_primary_10_3390_epigenomes9010005 crossref_primary_10_1016_j_crmeth_2022_100288 crossref_primary_10_1016_j_eururo_2023_05_037 crossref_primary_10_1021_acs_jproteome_4c01067 crossref_primary_10_1016_j_cell_2024_01_027 crossref_primary_10_1038_s41588_024_01662_5 crossref_primary_10_3390_cimb46030109 crossref_primary_10_1038_s41388_021_01681_0 crossref_primary_10_1038_s41467_024_53830_0 crossref_primary_10_1080_14789450_2020_1845654 crossref_primary_10_3390_ijms24098391 crossref_primary_10_26508_lsa_202201885 crossref_primary_10_3233_KCA_230012 crossref_primary_10_1016_j_isci_2024_111060 crossref_primary_10_1016_j_ccell_2022_12_001 crossref_primary_10_2147_JIR_S347732 crossref_primary_10_1038_s41467_024_54182_5 crossref_primary_10_1111_bju_15989 crossref_primary_10_1016_j_csbj_2022_12_005 crossref_primary_10_3390_cancers15061830 crossref_primary_10_1016_j_pathol_2022_07_013 crossref_primary_10_1053_j_akdh_2022_11_005 crossref_primary_10_1080_2162402X_2021_1993042 crossref_primary_10_1016_j_mcpro_2022_100263 crossref_primary_10_3389_fphar_2023_1213891 crossref_primary_10_1016_j_crmeth_2024_100708 crossref_primary_10_1073_pnas_2000516117 crossref_primary_10_2139_ssrn_4132721 crossref_primary_10_1007_s10142_024_01524_7 crossref_primary_10_1038_s41467_021_25202_5 crossref_primary_10_1158_1078_0432_CCR_23_1003 crossref_primary_10_1038_s41586_022_04499_2 crossref_primary_10_1002_path_5869 crossref_primary_10_1186_s13148_022_01319_2 crossref_primary_10_1146_annurev_pharmtox_022723_113921 crossref_primary_10_1016_j_eururo_2021_01_043 crossref_primary_10_1016_j_heliyon_2022_e10578 crossref_primary_10_3390_ijms24054488 crossref_primary_10_1016_j_ccell_2021_02_013 crossref_primary_10_1080_14789450_2024_2334033 crossref_primary_10_2217_fon_2023_0434 crossref_primary_10_1128_jmbe_00167_21 crossref_primary_10_3389_fimmu_2022_798471 crossref_primary_10_3389_fcell_2023_1168462 crossref_primary_10_1172_JCI164249 crossref_primary_10_1038_s41392_021_00729_7 crossref_primary_10_1002_cai2_25 crossref_primary_10_1016_j_celrep_2020_108276 crossref_primary_10_1039_D4MO00163J crossref_primary_10_1080_14789450_2021_1962300 crossref_primary_10_1016_j_intimp_2024_113147 crossref_primary_10_1136_jitc_2020_001823 crossref_primary_10_1073_pnas_2115999119 crossref_primary_10_1016_j_mcpro_2021_100062 crossref_primary_10_1038_s41467_022_34460_w crossref_primary_10_1016_j_mcpro_2023_100536 crossref_primary_10_1038_s41598_022_17755_2 crossref_primary_10_1016_j_mcpro_2023_100538 crossref_primary_10_1038_s41467_023_41374_8 crossref_primary_10_1186_s13059_024_03435_z crossref_primary_10_1002_mco2_261 crossref_primary_10_3389_fphar_2023_1038457 crossref_primary_10_1038_s41467_021_25872_1 crossref_primary_10_1038_s41568_022_00446_5 crossref_primary_10_1186_s13148_020_00998_z crossref_primary_10_1016_j_ccell_2022_11_001 crossref_primary_10_3389_fimmu_2021_745945 crossref_primary_10_1038_s41598_020_72107_2 crossref_primary_10_1016_j_scib_2023_09_029 crossref_primary_10_1093_narcan_zcaa015 crossref_primary_10_3390_ijms21072493 crossref_primary_10_1016_j_mcpro_2021_100171 crossref_primary_10_3389_fimmu_2023_1095195 crossref_primary_10_1016_j_mcpro_2023_100603 crossref_primary_10_1093_gigascience_giae113 crossref_primary_10_1002_2211_5463_13085 crossref_primary_10_3390_jpm13020295 crossref_primary_10_1038_s41586_023_06682_5 crossref_primary_10_1016_j_cell_2023_07_014 crossref_primary_10_1016_j_cell_2023_07_013 crossref_primary_10_1093_bib_bbac091 crossref_primary_10_1021_acs_jproteome_0c00919 crossref_primary_10_1016_j_apsb_2024_06_028 crossref_primary_10_1038_s41581_023_00800_2 crossref_primary_10_1016_j_ccell_2023_07_013 crossref_primary_10_1093_bib_bbac096 crossref_primary_10_1186_s13062_024_00576_w crossref_primary_10_1038_s41467_020_19045_9 crossref_primary_10_1016_j_cell_2023_07_004 crossref_primary_10_1038_s41592_020_0912_y crossref_primary_10_3390_jcm12010384 crossref_primary_10_1021_acs_jproteome_3c00526 crossref_primary_10_1002_ctm2_538 crossref_primary_10_15252_msb_202110631 crossref_primary_10_1002_pmic_202200238 crossref_primary_10_1016_j_tranon_2021_101078 crossref_primary_10_1093_narcan_zcad035 crossref_primary_10_1084_jem_20191005 crossref_primary_10_3390_biomedicines12010149 crossref_primary_10_1016_j_celrep_2021_108787 crossref_primary_10_1177_10668969231157317 crossref_primary_10_1016_j_cell_2020_10_044 crossref_primary_10_3389_fimmu_2021_765898 crossref_primary_10_1016_j_mcpro_2023_100626 crossref_primary_10_1038_s41375_024_02263_1 crossref_primary_10_1016_j_xcrm_2023_101315 crossref_primary_10_1186_s12967_023_04818_9 crossref_primary_10_1016_j_ijnss_2019_12_008 crossref_primary_10_2174_0113862073258779231020052115 crossref_primary_10_1016_j_celrep_2021_109866 crossref_primary_10_1177_10668969221125793 crossref_primary_10_1186_s12935_020_01242_7 crossref_primary_10_1007_s12672_024_01071_4 crossref_primary_10_1038_s41598_022_15206_6 crossref_primary_10_1093_neuonc_noaf033 crossref_primary_10_1002_pmic_202100369 crossref_primary_10_1016_j_clgc_2025_102318 crossref_primary_10_1038_s41698_024_00708_5 crossref_primary_10_1021_acs_jproteome_1c00657 crossref_primary_10_1038_s41598_022_13148_7 crossref_primary_10_1158_1078_0432_CCR_22_0921 crossref_primary_10_3389_fonc_2022_786981 crossref_primary_10_1038_s41467_024_49986_4 crossref_primary_10_3389_fonc_2023_1131191 crossref_primary_10_1016_j_ccell_2021_12_006 crossref_primary_10_1016_j_ccell_2022_06_010 crossref_primary_10_1038_s41467_023_39869_5 crossref_primary_10_3390_cancers16030478 crossref_primary_10_3389_fmed_2021_747333 crossref_primary_10_1016_j_tips_2020_02_005 crossref_primary_10_32604_biocell_2021_017369 crossref_primary_10_3389_fcell_2021_772436 crossref_primary_10_1016_j_tranon_2023_101726 crossref_primary_10_1038_s41585_022_00571_8 crossref_primary_10_1093_bib_bbab084 crossref_primary_10_1016_j_mcpro_2023_100596 crossref_primary_10_1159_000530719 crossref_primary_10_1158_0008_5472_CAN_23_0604 crossref_primary_10_1186_s13046_025_03301_1 crossref_primary_10_1016_j_mcpro_2025_100919 crossref_primary_10_1016_j_phrs_2021_105732 crossref_primary_10_1016_j_phrs_2023_106941 crossref_primary_10_1021_acs_jproteome_4c00911 crossref_primary_10_1016_j_ccell_2023_07_007 crossref_primary_10_1186_s40170_021_00271_8 crossref_primary_10_1158_1541_7786_MCR_21_0004 crossref_primary_10_1016_j_cell_2021_02_055 crossref_primary_10_1186_s12890_023_02452_1 crossref_primary_10_3389_fonc_2021_712765 crossref_primary_10_1016_j_heliyon_2024_e37897 crossref_primary_10_1038_s41596_024_01000_3 crossref_primary_10_1016_j_jncc_2023_08_003 crossref_primary_10_1021_acs_jproteome_0c00898 crossref_primary_10_1186_s12014_022_09359_9 crossref_primary_10_1038_s42003_021_02007_2 crossref_primary_10_1186_s13073_022_01105_y crossref_primary_10_1016_j_lfs_2021_120056 crossref_primary_10_3390_plants12061290 crossref_primary_10_1038_s44321_024_00077_3 crossref_primary_10_1002_imt2_147 crossref_primary_10_1007_s12672_024_01485_0 crossref_primary_10_1016_j_compbiolchem_2024_108282 crossref_primary_10_1186_s12882_022_02801_y crossref_primary_10_1021_acs_analchem_2c03299 crossref_primary_10_1038_s41467_025_57993_2 crossref_primary_10_1038_s41598_022_08430_7 crossref_primary_10_1371_journal_pcbi_1010702 crossref_primary_10_1186_s12885_023_10970_8 crossref_primary_10_1016_j_gpb_2021_08_012 crossref_primary_10_1158_0008_5472_CAN_23_0821 crossref_primary_10_1096_fj_202101310R crossref_primary_10_1155_2021_9997185 crossref_primary_10_1038_s41598_020_79049_9 crossref_primary_10_1097_MD_0000000000029561 crossref_primary_10_3389_fcell_2021_676142 crossref_primary_10_1038_s41598_024_51889_9 crossref_primary_10_3390_cimb46050279 crossref_primary_10_1016_j_mcpro_2023_100687 crossref_primary_10_1186_s12014_020_09283_w crossref_primary_10_1002_2211_5463_13487 crossref_primary_10_1155_2021_2148820 crossref_primary_10_1016_j_prp_2024_155324 crossref_primary_10_1016_j_tranon_2022_101420 crossref_primary_10_3389_fonc_2021_630842 crossref_primary_10_3390_cancers14030644 crossref_primary_10_1093_carcin_bgae033 crossref_primary_10_1093_bib_bbab163 crossref_primary_10_3389_fonc_2021_709579 crossref_primary_10_1038_s41401_022_01017_y crossref_primary_10_1080_01621459_2022_2110876 crossref_primary_10_3390_antiox12010081 crossref_primary_10_1016_j_eururo_2021_04_019 crossref_primary_10_1186_s12957_023_03013_w crossref_primary_10_1186_s12935_020_01576_2 crossref_primary_10_1038_s41698_024_00519_8 crossref_primary_10_2147_IJGM_S312416 crossref_primary_10_1038_s41418_023_01176_3 crossref_primary_10_3389_fgene_2023_1096491 crossref_primary_10_1186_s12864_023_09416_z crossref_primary_10_1038_s41571_020_00455_z crossref_primary_10_1016_j_mcpro_2023_100587 crossref_primary_10_52601_bpr_2024_240053 crossref_primary_10_1016_j_ccell_2020_10_011 crossref_primary_10_1016_j_heliyon_2023_e16479 crossref_primary_10_1016_j_celrep_2024_114103 crossref_primary_10_1038_s41419_023_06057_8 crossref_primary_10_1093_bib_bbad480 crossref_primary_10_1016_j_addr_2021_113844 crossref_primary_10_1002_path_6006 crossref_primary_10_3390_genes12030388 crossref_primary_10_1038_s41585_022_00659_1 crossref_primary_10_1016_j_eururo_2020_02_029 crossref_primary_10_1021_acs_jproteome_0c00984 |
| Cites_doi | 10.1016/j.yexcr.2013.07.022 10.1021/ac0262560 10.1038/nrc3130 10.1016/j.molmed.2013.05.002 10.1146/annurev-pathol-012414-040306 10.1158/2159-8290.CD-14-0673 10.1038/nrd.2018.21 10.1038/ncomms11884 10.1038/s41591-018-0053-3 10.1074/mcp.M115.056226 10.1371/journal.pcbi.1003790 10.1016/j.eururo.2018.06.007 10.1158/2159-8290.CD-17-1246 10.1038/ng.2891 10.1093/bioinformatics/btn323 10.1093/bioinformatics/btp394 10.1101/gad.279737.116 10.1186/gb-2011-12-1-r1 10.1016/j.sigpro.2004.11.012 10.1016/j.celrep.2017.07.043 10.4161/cbt.8.14.8880 10.1038/ncb1547 10.4049/jimmunol.1700893 10.1016/j.devcel.2014.11.016 10.1200/JCO.2018.79.2549 10.1038/nmeth.4256 10.1038/nrc.2017.104 10.1158/1078-0432.CCR-14-1128 10.3389/fimmu.2018.00414 10.1016/j.imbio.2011.10.016 10.1056/NEJMoa1505917 10.3109/1354750X.2013.811538 10.1016/j.cell.2016.05.069 10.1016/j.ccell.2017.02.008 10.1038/nature12222 10.1002/path.5022 10.1186/s13045-015-0180-y 10.1016/j.tips.2016.06.006 10.1016/j.molmed.2013.03.005 10.3390/cancers3044010 10.1093/bioinformatics/bty770 10.1016/j.cell.2018.03.057 10.1111/j.2517-6161.1995.tb02031.x 10.18632/oncotarget.7142 10.1016/S0140-6736(07)61904-7 10.1056/NEJMoa066838 10.1038/ng.2708 10.1172/JCI121476 10.1038/sj.onc.1203938 10.1016/S1470-2045(12)70584-3 10.1200/JCO.2009.23.9764 10.1038/nmeth.4075 10.1002/gcc.10209 10.1021/acs.jproteome.5b00925 10.1002/pmic.201000752 10.1016/j.cell.2018.03.043 10.1038/nbt.2514 10.1093/nar/28.1.27 10.1101/gr.129684.111 10.1056/NEJMoa1712126 10.1093/bioinformatics/btx378 10.1016/j.celrep.2016.02.024 10.1016/j.ccr.2007.07.006 10.1093/gigascience/gix054 10.3322/caac.21442 10.1101/gr.235028.118 10.1186/2193-1801-3-694 10.1093/bioinformatics/btq596 10.1038/ncomms15770 10.1016/S1388-1981(02)00364-5 10.1093/nar/gkx356 10.1172/jci.insight.121522 10.1038/ng.1014 10.1093/nar/27.1.29 10.1016/j.urolonc.2017.01.002 10.3390/molecules23040908 10.1145/366573.366611 10.1073/pnas.0506580102 10.1186/s13059-014-0503-2 10.1158/0008-5472.CAN-12-0366 10.1038/nature18003 10.1093/bioinformatics/btv268 10.1073/pnas.091062498 10.1038/nmeth.3255 10.1016/j.critrevonc.2015.08.007 10.1021/ac301553x 10.1074/mcp.M114.046995 10.1200/JCO.2007.14.5029 10.1038/nbt.2203 10.1093/nar/gku1267 10.1101/gr.1239303 10.1093/bioinformatics/btu548 10.1161/CIRCRESAHA.117.310696 10.1016/j.cell.2018.03.034 10.1016/j.ccr.2008.10.016 10.1021/ac025747h 10.1093/bib/bbu026 10.1093/bioinformatics/btr260 10.1056/NEJMoa065044 10.1083/jcb.92.2.584 10.1186/s13059-017-1349-1 10.1016/j.ccell.2015.12.004 10.1093/bioinformatics/btv710 10.1038/ncomms10975 10.1038/nrm2203 10.1038/s41467-018-05812-2 10.1093/nar/gkv1507 10.1186/1471-2105-14-7 10.1186/s13029-016-0060-z 10.1634/theoncologist.2015-0151 10.1038/nature13438 10.1126/science.1262110 10.1038/ncomms3612 10.1093/bioinformatics/bty280 10.1016/j.celrep.2018.03.075 10.1186/s12920-015-0108-y 10.1038/ncomms14864 10.1021/pr201052x 10.1038/nature08109 10.1038/s41467-018-03309-6 10.1186/1471-2105-12-436 10.1016/j.cancergen.2015.02.008 10.1186/gb-2014-15-6-r84 10.1021/ac0341261 10.1021/acs.jproteome.8b00165 10.1016/j.cmet.2006.01.012 10.1038/s41596-018-0006-9 10.1038/s41592-018-0051-x 10.1093/carcin/bgn125 10.1158/2159-8290.CD-11-0098 10.1016/j.ccr.2007.02.006 10.1038/cr.2014.10 10.1158/0008-5472.CAN-07-5311 10.1158/1078-0432.CCR-15-2631 10.1016/j.cell.2018.10.038 10.1016/j.cell.2018.02.020 10.1038/nrdp.2017.9 10.1038/s41467-018-03347-0 10.1158/0008-5472.CAN-05-0043 10.12688/f1000research.8923.1 10.1093/nar/gki072 10.1093/biostatistics/kxj037 10.1038/ncomms6277 10.3390/cancers7040902 10.1186/gb-2011-12-4-r41 10.1002/cpbi.47 10.1023/A:1023949509487 10.12688/f1000research.8839.2 10.1038/sj.onc.1201968 10.1155/2014/735292 10.1038/nature23306 10.1074/mcp.M400129-MCP200 10.1038/nature21349 10.1002/prca.201400164 10.1038/nrneph.2017.59 10.1016/j.ccell.2018.10.007 10.1158/2159-8290.CD-16-0267 10.1016/j.ccr.2010.05.023 10.1097/PAS.0000000000001150 10.1158/0008-5472.CAN-15-2478 10.1016/j.ccr.2014.07.014 10.1038/nrg2223 10.1021/ac301572t 10.1093/bioinformatics/btw691 10.1093/bioinformatics/btq170 10.1038/nature05571 10.1093/carcin/bgs177 10.1038/sj.bjc.6604208 10.1038/nmeth.2518 10.2147/OTT.S137677 10.1016/j.ctrv.2018.07.009 10.1016/j.celrep.2017.04.031 10.1158/2159-8290.CD-17-1033 10.1016/S1470-2045(13)70024-X 10.1158/2326-6066.CIR-15-0225 10.1056/NEJMoa060655 10.1016/S0140-6736(08)61039-9 10.1021/pr500880b 10.1021/pr200766z 10.1093/nar/gkw227 10.1074/mcp.RA118.001220 |
| ContentType | Journal Article |
| Contributor | Zhu, Heng Mani, D R Dyer, Maureen Robinson, Karna Elburn, Kim Gritsenko, Marina A Castro, Patricia Hoadley, Katherine A Birger, Chet Chaikin, Michelle Holloway, Kimberly Tansil, Darlene Vatanian, Negin Gao, Qingsong Ittmann, Michael M Modugno, Francesmary Borucki, Melissa Pico, Alexander R Zhu, Jun Chesla, David McGee, John Malovannaya, Anna Domagalski, Marcin J Kim, Beom-Jun Jones, Corbin D Eschbacher, Jennifer Hindenach, Barbara Blumenberg, Lili Perou, Amy M Sun, Hua Tyner, Jeffrey W Cornwell, MacIntosh Wang, Liang-Bo Hariharan, Pushpa Smith, Michael Qi, Liqun Culpepper, Houston Birrer, Michael J Grady, Pamela Thangudu, Ratna R Heiman, David Paulovich, Amanda G Vernon, Michael Wheeler, David Burke, Meghan C Demir, Emek Hannick, Linda Day, Jacob Montgomery, Rebecca Marrero-Oliveras, Annette Chheda, Milan G Rohrer, Daniel C Huang, Jasmine Edwards, Nathan J Lewis, Michael McDermott, Jason Kothadia, Ramani Bhupendra Druker, Brian J Gillette, Michael A Tognon, Cristina Whiteaker, Jeffrey R Rodland, Karin D Liu, Hongwei Chen, Jin McGarvey, Peter B Claus |
| Contributor_xml | – sequence: 1 givenname: Abdul Samad surname: Hashimi fullname: Hashimi, Abdul Samad – sequence: 2 givenname: Alexander R surname: Pico fullname: Pico, Alexander R – sequence: 3 givenname: Alla surname: Karpova fullname: Karpova, Alla – sequence: 4 givenname: Alyssa surname: Charamut fullname: Charamut, Alyssa – sequence: 5 givenname: Amanda G surname: Paulovich fullname: Paulovich, Amanda G – sequence: 6 givenname: Amy M surname: Perou fullname: Perou, Amy M – sequence: 7 givenname: Anna surname: Malovannaya fullname: Malovannaya, Anna – sequence: 8 givenname: Annette surname: Marrero-Oliveras fullname: Marrero-Oliveras, Annette – sequence: 9 givenname: Anupriya surname: Agarwal fullname: Agarwal, Anupriya – sequence: 10 givenname: Barbara surname: Hindenach fullname: Hindenach, Barbara – sequence: 11 givenname: Barbara surname: Pruetz fullname: Pruetz, Barbara – sequence: 12 givenname: Beom-Jun surname: Kim fullname: Kim, Beom-Jun – sequence: 13 givenname: Brian J surname: Druker fullname: Druker, Brian J – sequence: 14 givenname: Chelsea J surname: Newton fullname: Newton, Chelsea J – sequence: 15 givenname: Chet surname: Birger fullname: Birger, Chet – sequence: 16 givenname: Corbin D surname: Jones fullname: Jones, Corbin D – sequence: 17 givenname: Cristina surname: Tognon fullname: Tognon, Cristina – sequence: 18 givenname: D R surname: Mani fullname: Mani, D R – sequence: 19 givenname: Dana R surname: Valley fullname: Valley, Dana R – sequence: 20 givenname: Daniel C surname: Rohrer fullname: Rohrer, Daniel C – sequence: 21 givenname: Daniel C surname: Zhou fullname: Zhou, Daniel C – sequence: 22 givenname: Darlene surname: Tansil fullname: Tansil, Darlene – sequence: 23 givenname: David surname: Chesla fullname: Chesla, David – sequence: 24 givenname: David surname: Heiman fullname: Heiman, David – sequence: 25 givenname: David surname: Wheeler fullname: Wheeler, David – sequence: 26 givenname: Donghui surname: Tan fullname: Tan, Donghui – sequence: 27 givenname: Doug surname: Chan fullname: Chan, Doug – sequence: 28 givenname: Emek surname: Demir fullname: Demir, Emek – sequence: 29 givenname: Ewa surname: Malc fullname: Malc, Ewa – sequence: 30 givenname: Francesmary surname: Modugno fullname: Modugno, Francesmary – sequence: 31 givenname: Gaddy surname: Getz fullname: Getz, Gaddy – sequence: 32 givenname: Galen surname: Hostetter fullname: Hostetter, Galen – sequence: 33 givenname: George D surname: Wilson fullname: Wilson, George D – sequence: 34 givenname: Gerald W surname: Hart fullname: Hart, Gerald W – sequence: 35 givenname: Heng surname: Zhu fullname: Zhu, Heng – sequence: 36 givenname: Hongwei surname: Liu fullname: Liu, Hongwei – sequence: 37 givenname: Houston surname: Culpepper fullname: Culpepper, Houston – sequence: 38 givenname: Hua surname: Sun fullname: Sun, Hua – sequence: 39 givenname: Hua surname: Zhou fullname: Zhou, Hua – sequence: 40 givenname: Jacob surname: Day fullname: Day, Jacob – sequence: 41 givenname: James surname: Suh fullname: Suh, James – sequence: 42 givenname: Jasmine surname: Huang fullname: Huang, Jasmine – sequence: 43 givenname: Jason surname: McDermott fullname: McDermott, Jason – sequence: 44 givenname: Jeffrey R surname: Whiteaker fullname: Whiteaker, Jeffrey R – sequence: 45 givenname: Jeffrey W surname: Tyner fullname: Tyner, Jeffrey W – sequence: 46 givenname: Jennifer surname: Eschbacher fullname: Eschbacher, Jennifer – sequence: 47 givenname: Jin surname: Chen fullname: Chen, Jin – sequence: 48 givenname: John surname: McGee fullname: McGee, John – sequence: 49 givenname: Jun surname: Zhu fullname: Zhu, Jun – sequence: 50 givenname: Karen A surname: Ketchum fullname: Ketchum, Karen A – sequence: 51 givenname: Karin D surname: Rodland fullname: Rodland, Karin D – sequence: 52 givenname: Karl surname: Clauser fullname: Clauser, Karl – sequence: 53 givenname: Karna surname: Robinson fullname: Robinson, Karna – sequence: 54 givenname: Karsten surname: Krug fullname: Krug, Karsten – sequence: 55 givenname: Katherine A surname: Hoadley fullname: Hoadley, Katherine A – sequence: 56 givenname: Ki Sung surname: Um fullname: Um, Ki Sung – sequence: 57 givenname: Kim surname: Elburn fullname: Elburn, Kim – sequence: 58 givenname: Kimberly surname: Holloway fullname: Holloway, Kimberly – sequence: 59 givenname: Liang-Bo surname: Wang fullname: Wang, Liang-Bo – sequence: 60 givenname: Lili surname: Blumenberg fullname: Blumenberg, Lili – sequence: 61 givenname: Linda surname: Hannick fullname: Hannick, Linda – sequence: 62 givenname: Liqun surname: Qi fullname: Qi, Liqun – sequence: 63 givenname: Lori J surname: Sokoll fullname: Sokoll, Lori J – sequence: 64 givenname: MacIntosh surname: Cornwell fullname: Cornwell, MacIntosh – sequence: 65 givenname: Marc surname: Loriaux fullname: Loriaux, Marc – sequence: 66 givenname: Marcin J surname: Domagalski fullname: Domagalski, Marcin J – sequence: 67 givenname: Marina A surname: Gritsenko fullname: Gritsenko, Marina A – sequence: 68 givenname: Matthew surname: Anderson fullname: Anderson, Matthew – sequence: 69 givenname: Matthew E surname: Monroe fullname: Monroe, Matthew E – sequence: 70 givenname: Matthew J surname: Ellis fullname: Ellis, Matthew J – sequence: 71 givenname: Maureen surname: Dyer fullname: Dyer, Maureen – sequence: 72 givenname: Meenakshi surname: Anurag fullname: Anurag, Meenakshi – sequence: 73 givenname: Meghan C surname: Burke fullname: Burke, Meghan C – sequence: 74 givenname: Melissa surname: Borucki fullname: Borucki, Melissa – sequence: 75 givenname: Michael A surname: Gillette fullname: Gillette, Michael A – sequence: 76 givenname: Michael J surname: Birrer fullname: Birrer, Michael J – sequence: 77 givenname: Michael surname: Lewis fullname: Lewis, Michael – sequence: 78 givenname: Michael M surname: Ittmann fullname: Ittmann, Michael M – sequence: 79 givenname: Michael surname: Smith fullname: Smith, Michael – sequence: 80 givenname: Michael surname: Vernon fullname: Vernon, Michael – sequence: 81 givenname: Michelle surname: Chaikin fullname: Chaikin, Michelle – sequence: 82 givenname: Milan G surname: Chheda fullname: Chheda, Milan G – sequence: 83 givenname: Munziba surname: Khan fullname: Khan, Munziba – sequence: 84 givenname: Nancy surname: Roche fullname: Roche, Nancy – sequence: 85 givenname: Nathan J surname: Edwards fullname: Edwards, Nathan J – sequence: 86 givenname: Negin surname: Vatanian fullname: Vatanian, Negin – sequence: 87 givenname: Nicole surname: Tignor fullname: Tignor, Nicole – sequence: 88 givenname: Noam surname: Beckmann fullname: Beckmann, Noam – sequence: 89 givenname: Pamela surname: Grady fullname: Grady, Pamela – sequence: 90 givenname: Patricia surname: Castro fullname: Castro, Patricia – sequence: 91 givenname: Paul surname: Piehowski fullname: Piehowski, Paul – sequence: 92 givenname: Peter B surname: McGarvey fullname: McGarvey, Peter B – sequence: 93 givenname: Piotr surname: Mieczkowski fullname: Mieczkowski, Piotr – sequence: 94 givenname: Pushpa surname: Hariharan fullname: Hariharan, Pushpa – sequence: 95 givenname: Qingsong surname: Gao fullname: Gao, Qingsong – sequence: 96 givenname: Rajiv surname: Dhir fullname: Dhir, Rajiv – sequence: 97 givenname: Ramani Bhupendra surname: Kothadia fullname: Kothadia, Ramani Bhupendra – sequence: 98 givenname: Ratna R surname: Thangudu fullname: Thangudu, Ratna R – sequence: 99 givenname: Rebecca surname: Montgomery fullname: Montgomery, Rebecca – sequence: 100 givenname: Reyka G surname: Jayasinghe fullname: Jayasinghe, Reyka G |
| Copyright | 2019 Elsevier Inc. Copyright © 2019 Elsevier Inc. All rights reserved. |
| Copyright_xml | – notice: 2019 Elsevier Inc. – notice: Copyright © 2019 Elsevier Inc. All rights reserved. |
| CorporateAuthor | Clinical Proteomic Tumor Analysis Consortium |
| CorporateAuthor_xml | – name: Clinical Proteomic Tumor Analysis Consortium |
| DBID | 6I. AAFTH AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6 5PM |
| DOI | 10.1016/j.cell.2019.10.007 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | MEDLINE - Academic AGRICOLA MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1097-4172 |
| EndPage | 983.e31 |
| ExternalDocumentID | PMC7331093 31675502 10_1016_j_cell_2019_10_007 S0092867419311237 |
| Genre | Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NIGMS NIH HHS grantid: R01 GM108711 – fundername: NCI NIH HHS grantid: U24 CA210955 – fundername: NCI NIH HHS grantid: U24 CA210993 – fundername: NCI NIH HHS grantid: T32 CA140044 – fundername: NCI NIH HHS grantid: U24 CA210967 – fundername: NCI NIH HHS grantid: P30 CA008748 – fundername: NCI NIH HHS grantid: U24 CA210985 |
| GroupedDBID | --- --K -DZ -ET -~X 0R~ 0WA 1RT 1~5 29B 2FS 2WC 3EH 4.4 457 4G. 53G 5GY 5RE 62- 6I. 6J9 7-5 85S AACTN AAEDT AAEDW AAFTH AAFWJ AAHBH AAKRW AAKUH AALRI AAMRU AAVLU AAXUO ABCQX ABJNI ABMAC ABOCM ACGFO ACGFS ACNCT ADBBV ADEZE ADVLN AEFWE AENEX AEXQZ AFTJW AGHSJ AGKMS AHHHB AITUG AKAPO AKRWK ALMA_UNASSIGNED_HOLDINGS AMRAJ ASPBG AVWKF AZFZN BAWUL CS3 DIK DU5 E3Z EBS EJD F5P FCP FDB FIRID HH5 IH2 IHE IXB J1W JIG K-O KOO KQ8 L7B LX5 M3Z M41 N9A O-L O9- OK1 P2P RIG RNS ROL RPZ SCP SDG SDP SES SSZ TAE TN5 TR2 TWZ UKR UPT WH7 YZZ ZCA .-4 .55 .GJ .HR 1CY 1VV 2KS 3O- 5VS 6TJ 9M8 AAIKJ AAQFI AAQXK AAYJJ AAYWO AAYXX ABDGV ABDPE ABEFU ABWVN ACRPL ACVFH ADCNI ADMUD ADNMO ADXHL AETEA AEUPX AFPUW AGCQF AGHFR AGQPQ AI. AIDAL AIGII AKBMS AKYEP APXCP CITATION FEDTE FGOYB G-2 HVGLF HZ~ H~9 MVM OHT OMK OZT PUQ R2- UBW UHB VH1 X7M YYP YYQ ZGI ZHY ZKB ZY4 CGR CUY CVF ECM EFKBS EIF NPM 7X8 7S9 L.6 5PM |
| ID | FETCH-LOGICAL-c554t-ff905f45cb0d69fc048bb74f25af43bf3f0e5ff7a41005380afafdb2228753b13 |
| IEDL.DBID | IXB |
| ISSN | 0092-8674 1097-4172 |
| IngestDate | Thu Aug 21 18:29:54 EDT 2025 Sun Sep 28 02:25:46 EDT 2025 Sun Sep 28 02:50:37 EDT 2025 Mon Jul 21 06:04:36 EDT 2025 Tue Jul 01 02:17:05 EDT 2025 Thu Apr 24 22:53:12 EDT 2025 Sun Apr 06 06:54:12 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Keywords | phosphoproteomics ccRCC renal carcinoma proteomics immune infiltration drug targets tumor microenvironment CPTAC proteogenomics chromosomal translocation |
| Language | English |
| License | This is an open access article under the CC BY license. Copyright © 2019 Elsevier Inc. All rights reserved. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c554t-ff905f45cb0d69fc048bb74f25af43bf3f0e5ff7a41005380afafdb2228753b13 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AUTHOR CONTRIBUTIONS Conceptualization, H.R., D.C., A.I.N., P.W., and H.Z.; Methodology, D.J.C. and L.C.; Software, F.P., J.P., X.S., Y.H., F.d.V.L., B.R., T.-S.M.L., H.-Y.C., W.M., C.H., A. Krek, Y.L., D.R., L.S.C., U.O., S.V., S.Y., S. Chowdhury, J.J., A. Kong, S.S., D.M.A., N.E., Z.Z., M.C., A.I.N., and P.W.; Validation, S.M.D., K.L.Q., and K.-C.C.; Formal Analysis, D.J.C., S.M.D., F.P., J.P., X.S., Y.H., B.R., T.-S.M.L., H.-Y.C., W.M., C.H., A. Krek, Y.L., D.R., L.S.C., U.O., S.V., Y.W., S.Y., S. Chowdhury, J.J., A. Kong, S.S., D.M.A., A. Colaprico, S. Cao, S. Kalayci, S.M., W.L., K.R., D.G., E.K., G.C.T., B.W., Y.Z., S. Keegan, K.L., F.C., N.E., A.I.N., P.W., and H.Z.; Investigation, D.J.C., L.C., M.S., K.-C.C., D.W.C., and H.Z.; Resources, Q.K.L., C.P.P., G.B., A.A., J.L., and M.T.; Data Curation, D.J.C., S.M.D., W.M., M.A.W., M.S., M.A., M.C., A.I.N., P.W., and H.Z.; Writing – Original Draft, D.J.C., A.I.N., P.W., and H.Z.; Writing – Review & Editing, all authors; Visualization, D.J.C., S.M.D., F.P., J.P., X.S., Y.H., B.R., T.-S.M.L., C.H., C.J.R., A. Krek, Y.L., D.R., U.O., S.V., M.A., A. Calinawan, Z.H.G., Y.Z., and M.C.; Supervision, D.J.C., S.M.D., C.J.R., P.M.P., X.S.C., C.P.P., A.A.H, G.B., J.H., A.A., T.O., J.L., M.W., W.M.L., J.Q., D.F., B.Z., L.D., E.S., A.M.C., Z.Z., G.S.O., D.W.C., A.I.N., P.W., and H.Z.; Project Administration, D.J.C., C.R.K., M.T., M.M., E.S.B., M.M., T.H., A.I.R., H.R., D.W.C., A.I.N., P.W., and H.Z.; Funding Acquisition, B.Z., L.D., D.F., E.S., A.M.C., Z.Z., D.W.C., A.I.N., P.W., and H.Z. |
| OpenAccessLink | https://www.sciencedirect.com/science/article/pii/S0092867419311237 |
| PMID | 31675502 |
| PQID | 2311656834 |
| PQPubID | 23479 |
| PageCount | 20 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_7331093 proquest_miscellaneous_2374194417 proquest_miscellaneous_2311656834 pubmed_primary_31675502 crossref_citationtrail_10_1016_j_cell_2019_10_007 crossref_primary_10_1016_j_cell_2019_10_007 elsevier_sciencedirect_doi_10_1016_j_cell_2019_10_007 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2019-10-31 |
| PublicationDateYYYYMMDD | 2019-10-31 |
| PublicationDate_xml | – month: 10 year: 2019 text: 2019-10-31 day: 31 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Cell |
| PublicationTitleAlternate | Cell |
| PublicationYear | 2019 |
| Publisher | Elsevier Inc |
| Publisher_xml | – name: Elsevier Inc |
| References | Garcia-Diaz, Shin, Moreno, Saco, Escuin-Ordinas, Rodriguez, Zaretsky, Sun, Hugo, Wang (bib47) 2017; 19 Escudier, Pluzanska, Koralewski, Ravaud, Bracarda, Szczylik, Chevreau, Filipek, Melichar, Bajetta (bib42) 2007; 370 Kanehisa, Goto (bib77) 2000; 28 Aran, Hu, Butte (bib5) 2017; 18 Deutsch, Mendoza, Shteynberg, Slagel, Sun, Moritz (bib34) 2015; 9 McDermott, Huseni, Atkins, Motzer, Rini, Escudier, Fong, Joseph, Pal, Reeves (bib101) 2018; 24 Riester, Singh, Brannon, Yu, Campbell, Chiang, Morrissey (bib142) 2016; 11 Szolek, Schubert, Mohr, Sturm, Feldhahn, Kohlbacher (bib165) 2014; 30 Gerlinger, Horswell, Larkin, Rowan, Salm, Varela, Fisher, McGranahan, Matthews, Santos (bib50) 2014; 46 Gordan, Bertout, Hu, Diehl, Simon (bib52) 2007; 11 Komili, Silver (bib79) 2008; 9 Panda, de Cubas, Stein, Riedlinger, Kra, Mayer, Smith, Vincent, Serody, Beckermann (bib125) 2018; 3 Fortin, Labbe, Lemire, Zanke, Hudson, Fertig, Greenwood, Hansen (bib45) 2014; 15 Ricketts, De Cubas, Fan, Smith, Lang, Reznik, Bowlby, Gibb, Akbani, Beroukhim (bib141) 2018; 23 Lakins, Ghorani, Munir, Martins, Shields (bib83) 2018; 9 Nesvizhskii, Keller, Kolker, Aebersold (bib118) 2003; 75 Lih, Clark, Zhang (bib90) 2019 Bailey, Smith, Kardos, Wobker, Wilson, Krishnan, Saito, Lee, Zhang, Eaton (bib10) 2017; 8 Layer, Chiang, Quinlan, Hall (bib84) 2014; 15 McAlister, Huttlin, Haas, Ting, Jedrychowski, Rogers, Kuhn, Pike, Grothe, Blethrow, Gygi (bib100) 2012; 84 Pedregosa, Varoquaux, Gramfort, Michel, Thirion, Grisel, Blondel, Prettenhofer, Weiss, Dubourg (bib129) 2011; 12 Kessner, Chambers, Burke, Agus, Mallick (bib199) 2008; 24 Su, Kuchinsky, Morris, States, Meng (bib163) 2010; 26 Gordan, Thompson, Simon (bib53) 2007; 12 Carter, Cibulskis, Helman, McKenna, Shen, Zack, Laird, Onofrio, Winckler, Weir (bib22) 2012; 30 Sade-Feldman, Yizhak, Bjorgaard, Ray, de Boer, Jenkins, Lieb, Chen, Frederick, Barzily-Rokni (bib146) 2018; 175 Tsou, Avtonomov, Larsen, Tucholska, Choi, Gingras, Nesvizhskii (bib168) 2015; 12 Blanco, Teh, Amato (bib16) 2011; 3 Keller, Nesvizhskii, Kolker, Aebersold (bib78) 2002; 74 Krieg, Haas, Brauch, Acker, Flamme, Plate (bib81) 2000; 19 Atkins, Tannir (bib8) 2018; 70 Ogata, Goto, Sato, Fujibuchi, Bono, Kanehisa (bib120) 1999; 27 Naing, Infante, Papadopoulos, Chan, Shen, Ratti, Rojo, Autio, Wong, Patel (bib117) 2018; 34 Song, Ji, Gleason, Yang, Martignetti, Chen, Wang (bib160) 2019; 18 Ubersax, Ferrell (bib172) 2007; 8 Cao (bib20) 2013; 19 Siegel, Miller, Jemal (bib156) 2018; 68 Vander Haar, Lee, Bandhakavi, Griffin, Kim (bib173) 2007; 9 Hara, Miyake, Fujisawa (bib58) 2017; 35 Zhang, Liu, Zhang, Payne, Zhang, McDermott, Zhou, Petyuk, Chen, Ray (bib190) 2016; 166 Davis, Ricketts, Wang, Yang, Cherniack, Shen, Buhay, Kang, Kim, Fahey (bib32) 2014; 26 Kapur, Peña-Llopis, Christie, Zhrebker, Pavía-Jiménez, Rathmell, Xie, Brugarolas (bib198) 2013; 14 She, Halilovic, Ye, Zhen, Shirasawa, Sasazuki, Solit, Rosen (bib151) 2010; 18 Hsieh, Purdue, Signoretti, Swanton, Albiges, Schmidinger, Heng, Larkin, Ficarra (bib64) 2017; 3 Wen, Wang, Zhang (bib178) 2019; 29 Austen, Cerni, Lüscher-Firzlaff, Lüscher (bib9) 1998; 17 Monti, Tamayo, Mesirov, Golub (bib111) 2003; 52 Mertins, Mani, Ruggles, Gillette, Clauser, Wang, Wang, Qiao, Cao, Petralia (bib105) 2016; 534 Malta, Sokolov, Gentles, Burzykowski, Poisson, Weinstein, Kaminska, Huelsken, Omberg, Gevaert (bib205) 2018; 173 Wang, Slebos, Wang, Halvey, Tabb, Liebler, Zhang (bib174) 2012; 11 Werner, Becher, Sweetman, Doce, Savitski, Bantscheff (bib179) 2012; 84 Turajlic, Xu, Litchfield, Rowan, Chambers, Lopez, Nicol, O’Brien, Larkin, Horswell (bib170) 2018; 173 Huang, Ding, Luo, Bender, Qian, Kort, Zhang, VandenBeldt, Duesbery, Resau, Teh (bib68) 2008; 68 Petrella, Brinckerhoff (bib135) 2009; 8 Kim, Scheffler, Halpern, Bekritsky, Noh, Källberg, Chen, Kim, Beyter, Krusche (bib201) 2018; 15 Kwiatkowski, Choueiri, Fay, Rini, Thorner, de Velasco, Tyburczy, Hamieh, Albiges, Agarwal (bib82) 2016; 22 Petralia, Wang, Yang, Tu (bib132) 2015; 31 Wang, Vasaikar, Shi, Greer, Zhang (bib175) 2017; 45 Wilkerson, Hayes (bib182) 2010; 26 Pierre-Jean, Rigaill, Neuvial (bib136) 2015; 16 Ruggles, Tang, Wang, Grover, Askenazi, Teubl, Cao, McLellan, Clauser, Tabb (bib145) 2016; 15 Liao, Testa, Yang (bib88) 2015; 208 Rauniyar, Yates (bib138) 2014; 13 Creighton, Morgan, Gunaratne, Wheeler, Gibbs, Robertson, Chu, Beroukhim, Cibulskis, Signoretti (bib31) 2013; 499 Wang, Zhang, Chen, Skala, Al-Ahmadie, Wang, Cao, Veeneman, Chen, Cieślik (bib176) 2018; 42 Lindgren, Eriksson, Krawczyk, Nilsson, Hansson, Veerla, Sjölund, Höglund, Johansson, Axelson (bib93) 2017; 20 Lai, Markovets, Ahdesmaki, Chapman, Hofmann, Mcewen, Johnson, Dougherty, Barrett, Dry (bib203) 2016; 44 Liberzon, Subramanian, Pinchback, Thorvaldsdóttir, Tamayo, Mesirov (bib89) 2011; 27 Motzer, Hutson, Tomczak, Michaelson, Bukowski, Rixe, Oudard, Negrier, Szczylik, Kim (bib114) 2007; 356 Carles, Bourg, Meyer, Bonnet (bib21) 2018; 23 Ferguson, Gray (bib43) 2018; 17 Lebarbier (bib85) 2005; 85 Li, Vaudel, Zhang, Ren, Wen (bib87) 2019; 35 Hu, Ao, Zhang (bib67) 2019 Lusis, Watson, Chicoine, Lyman, Roerig, Reifenberger, Gutmann, Perry (bib96) 2005; 65 Hsieh, Le, Cao, Cheng, Creighton (bib66) 2018; 244 Anderson, Stromnes, Greenberg (bib2) 2017; 31 Seppä, Grotendorst, Seppä, Schiffmann, Martin (bib149) 1982; 92 Ross, Huang, Marchese, Williamson, Parker, Hattan, Khainovski, Pillai, Dey, Daniels (bib144) 2004; 3 Zhu, Ding, Qiu, Shi, Song, Wang, Wang, Li, Wang, Sun (bib192) 2017; 121 Mehra, Vats, Cieslik, Cao, Su, Shukla, Udager, Wang, Pan, Kasaian (bib206) 2016; 6 Linehan, Spellman, Ricketts, Creighton, Fei, Davis, Wheeler, Murray, Schmidt, Vocke (bib94) 2016; 374 Hein, Nilsson (bib59) 2016; 7 Maroto, Esteban, Parra, Mendez-Vidal, Domenech, Pérez-Valderrama, Calderero, Pérez-Gracia, Grande, Algaba (bib97) 2017; 10 Yoo, Huang, Campbell, Lee, Tu, Geraci, Powell, Schadt, Spira, Zhu (bib185) 2014; 10 Baylin, Jones (bib11) 2011; 11 Hogrebe, von Stechow, Bekker-Jensen, Weinert, Kelstrup, Olsen (bib62) 2018; 9 Motzer, Escudier, Oudard, Hutson, Porta, Bracarda, Grünwald, Thompson, Figlin, Hollaender (bib115) 2008; 372 Ardlie, Deluca, Segre, Sullivan, Young, Gelfand, Trowbridge, Maller, Tukiainen, Lek (bib194) 2015; 348 Luo, Chen, Chen, Alkam, Wang, Semenza (bib95) 2016; 7 Fisher, Barry, Abreu, Minie, Nolan, Delorey, Young, Fennell, Allen, Ambrogio (bib44) 2011; 12 Escudier, Eisen, Stadler, Szczylik, Oudard, Siebels, Negrier, Chevreau, Solska, Desai (bib41) 2007; 356 Mermel, Schumacher, Hill, Meyerson, Beroukhim, Getz (bib103) 2011; 12 Lehto, Olkkonen (bib86) 2003; 1631 Hsieh, Le, Oyama, Ricketts, Ho, Cheng (bib65) 2018; 36 Huang, Li, Mertins, Cao, Gunawardena, Ruggles, Mani, Clauser, Tanioka, Usary (bib69) 2017; 8 Chen, Diao, Yang, Yi, Rodriguez, Li, Villalobos, Cascone, Liu, Tan (bib27) 2018; 8 Hellström, Phng, Hofmann, Wallgard, Coultas, Lindblom, Alva, Nilsson, Karlsson, Gaiano (bib60) 2007; 445 Fortin, Triche, Hansen (bib196) 2017; 33 Hänzelmann, Castelo, Guinney (bib57) 2013; 14 Sokolov, Paull, Stuart (bib159) 2016; 21 Shannon, Markiel, Ozier, Baliga, Wang, Ramage, Amin, Schwikowski, Ideker (bib150) 2003; 13 Shin, Jeon, Cho, Lee, Chung, Park, Go (bib155) 2015; 20 Gey, Lebarbier (bib51) 2008; 12 Motzer, Tannir, McDermott, Arén Frontera, Melichar, Choueiri, Plimack, Barthélémy, Porta, George (bib116) 2018; 378 Turajlic, Xu, Litchfield, Rowan, Horswell, Chambers, O’Brien, Lopez, Watkins, Nicol (bib169) 2018; 173 Johnson, Li, Rabinovic (bib72) 2007; 8 Mgrditchian, Arakelian, Paggetti, Viry, Al-Absi, Medves, Moussay, Berchem, Thomas, Janji (bib107) 2014; 1 Beuselinck, Job, Becht, Karadimou, Verkarre, Couchy, Giraldo, Rioux-Leclercq, Molinié, Sibony (bib14) 2015; 21 Hervouet, Cízková, Demont, Vojtísková, Pecina, Franssen-van Hal, Keijer, Simonnet, Ivánek, Kmoch (bib61) 2008; 29 Ravaud, Hawkins, Gardner, von der Maase, Zantl, Harper, Rolland, Audhuy, Machiels, Pétavy (bib139) 2008; 26 Jurtz, Paul, Andreatta, Marcatili, Peters, Nielsen (bib75) 2017; 199 Clark, Hu, Bocik, Chen, Schnaubelt, Roberts, Shah, Whiteley, Zhang (bib29) 2018; 17 Frew, Moch (bib46) 2015; 10 Chen, Zhang, Şenbabaoğlu, Ciriello, Yang, Reznik, Shuch, Micevic, De Velasco, Shinbrot (bib25) 2016; 14 Shen, Beroukhim, Schumacher, Zhou, Chang, Signoretti, Kaelin (bib152) 2011; 1 Smith, Beckermann, Bortone, De Cubas, Bixby, Lee, Panda, Ganesan, Bhanot, Wallen (bib158) 2018; 128 Bellman (bib12) 1961; 4 Chrzanowska-Wodnicka (bib28) 2013; 319 Mitchell, Turajlic, Rowan, Nicol, Farmery, O’Brien, Martincorena, Tarpey, Angelopoulos, Yates (bib109) 2018; 173 Ishigami, Leite, Pakalniskis, Lee, Holanda, Kuehn (bib71) 2014; 3 Kong, Leprevost, Avtonomov, Mellacheruvu, Nesvizhskii (bib80) 2017; 14 Koboldt, Zhang, Larson, Shen, McLellan, Lin, Miller, Mardis, Ding, Wilson (bib202) 2012; 22 Hakimi, Reznik, Lee, Creighton, Brannon, Luna, Aksoy, Liu, Shen, Lee (bib56) 2016; 29 Scott, Kabbarah, Liang, Ivanova, Anagnostou, Wu, Dhakal, Wu, Chen, Feinberg (bib148) 2009; 459 Wang, Lu, Kapur, Jaiswal, Hannan, Zhang, Pedrosa, Luke, Zhang, Goldstein (bib177) 2018; 8 Chen, Schulz-Trieglaff, Shaw, Barnes, Schlesinger, Källberg, Cox, Kruglyak, Saunders (bib26) 2016; 32 Maksimovic, Phipson, Oshlack (bib204) 2016; 5 Lim, Li, Xia, Lee, Chang, Shen, Hsu, Raftery, Djukovic, Gu (bib92) 2016; 76 Petralia, Wang, Peng, Yan, Zhu, Wang (bib134) 2018; 34 Chen, Mellman (bib23) 2017; 541 Dmitriev, Rudenko, Kudryavtseva, Krasnov, Gordiyuk, Melnikova, Stakhovsky, Kononenko, Pavlova, Kondratieva (bib37) 2014; 2014 Argentini, Goeminne, Verheggen, Hulstaert, Staes, Clement, Martens (bib6) 2016; 13 Mertins, Qiao, Patel, Udeshi, Clauser, Mani, Burgess, Gillette, Jaffe, Carr (bib104) 2013; 10 Matsushita, Sato, Karasaki, Nakagawa, Kume, Ogawa, Homma, Kakimi (bib99) 2016; 4 Pan, Qian, Zhang (bib124) 2019 Robinson, Wu, Lonigro, Vats, Cobain, Everett, Cao, Rabban, Kumar-Sinha, Raymond (bib143) 2017; 548 Staedtler, Hartmann, Letzkus, Bongiovanni, Scherer, Marc, Johnson, Schumacher (bib161) 2013; 18 Xu, Le, Liu, Su, Wang, Sun, Colaprico, Bontempi, Li (bib184) 2017; 33 Cibulskis, Lawrence, Carter, Sivachenko, Jaffe, Sougnez, Gab Bailey (10.1016/j.cell.2019.10.007_bib10) 2017; 8 Hakimi (10.1016/j.cell.2019.10.007_bib197) 2013; 45 Sade-Feldman (10.1016/j.cell.2019.10.007_bib146) 2018; 175 Monti (10.1016/j.cell.2019.10.007_bib111) 2003; 52 Kalayci (10.1016/j.cell.2019.10.007_bib76) 2018; 61 Gey (10.1016/j.cell.2019.10.007_bib51) 2008; 12 Lindgren (10.1016/j.cell.2019.10.007_bib93) 2017; 20 Pavlovich (10.1016/j.cell.2019.10.007_bib128) 2003; 37 Atkins (10.1016/j.cell.2019.10.007_bib8) 2018; 70 Shiga (10.1016/j.cell.2019.10.007_bib154) 2015; 7 Hu (10.1016/j.cell.2019.10.007_bib67) 2019 Dmitriev (10.1016/j.cell.2019.10.007_bib37) 2014; 2014 Kwiatkowski (10.1016/j.cell.2019.10.007_bib82) 2016; 22 Ziani (10.1016/j.cell.2019.10.007_bib193) 2018; 9 Staedtler (10.1016/j.cell.2019.10.007_bib161) 2013; 18 Turajlic (10.1016/j.cell.2019.10.007_bib170) 2018; 173 Huang (10.1016/j.cell.2019.10.007_bib68) 2008; 68 Hellström (10.1016/j.cell.2019.10.007_bib60) 2007; 445 Bellman (10.1016/j.cell.2019.10.007_bib12) 1961; 4 Shin (10.1016/j.cell.2019.10.007_bib155) 2015; 20 Wang (10.1016/j.cell.2019.10.007_bib176) 2018; 42 Hein (10.1016/j.cell.2019.10.007_bib59) 2016; 7 Pelletier (10.1016/j.cell.2019.10.007_bib130) 2018; 18 Wu (10.1016/j.cell.2019.10.007_bib183) 2013; 73 Creighton (10.1016/j.cell.2019.10.007_bib31) 2013; 499 Wang (10.1016/j.cell.2019.10.007_bib174) 2012; 11 Sokolov (10.1016/j.cell.2019.10.007_bib159) 2016; 21 Linehan (10.1016/j.cell.2019.10.007_bib94) 2016; 374 Riester (10.1016/j.cell.2019.10.007_bib142) 2016; 11 Zhang (10.1016/j.cell.2019.10.007_bib190) 2016; 166 Chen (10.1016/j.cell.2019.10.007_bib26) 2016; 32 Gerlinger (10.1016/j.cell.2019.10.007_bib50) 2014; 46 Krieg (10.1016/j.cell.2019.10.007_bib81) 2000; 19 Hänzelmann (10.1016/j.cell.2019.10.007_bib57) 2013; 14 Hogrebe (10.1016/j.cell.2019.10.007_bib62) 2018; 9 Pan (10.1016/j.cell.2019.10.007_bib124) 2019 Hakimi (10.1016/j.cell.2019.10.007_bib56) 2016; 29 Baylin (10.1016/j.cell.2019.10.007_bib11) 2011; 11 Gordan (10.1016/j.cell.2019.10.007_bib53) 2007; 12 Yoshihara (10.1016/j.cell.2019.10.007_bib186) 2013; 4 Shenoy (10.1016/j.cell.2019.10.007_bib153) 2015; 8 Kessner (10.1016/j.cell.2019.10.007_bib199) 2008; 24 McAlister (10.1016/j.cell.2019.10.007_bib100) 2012; 84 Li (10.1016/j.cell.2019.10.007_bib87) 2019; 35 Ishigami (10.1016/j.cell.2019.10.007_bib71) 2014; 3 Hudes (10.1016/j.cell.2019.10.007_bib70) 2007; 356 Turajlic (10.1016/j.cell.2019.10.007_bib169) 2018; 173 Alyass (10.1016/j.cell.2019.10.007_bib1) 2015; 8 Motzer (10.1016/j.cell.2019.10.007_bib115) 2008; 372 Nesvizhskii (10.1016/j.cell.2019.10.007_bib118) 2003; 75 Lim (10.1016/j.cell.2019.10.007_bib92) 2016; 76 Cao (10.1016/j.cell.2019.10.007_bib20) 2013; 19 Chrzanowska-Wodnicka (10.1016/j.cell.2019.10.007_bib28) 2013; 319 Gascard (10.1016/j.cell.2019.10.007_bib48) 2016; 30 Tusher (10.1016/j.cell.2019.10.007_bib171) 2001; 98 Escudier (10.1016/j.cell.2019.10.007_bib42) 2007; 370 Lebarbier (10.1016/j.cell.2019.10.007_bib85) 2005; 85 Wettersten (10.1016/j.cell.2019.10.007_bib180) 2017; 13 Garcia-Diaz (10.1016/j.cell.2019.10.007_bib47) 2017; 19 Rauniyar (10.1016/j.cell.2019.10.007_bib138) 2014; 13 Ascierto (10.1016/j.cell.2019.10.007_bib7) 2013; 14 Luo (10.1016/j.cell.2019.10.007_bib95) 2016; 7 Werner (10.1016/j.cell.2019.10.007_bib179) 2012; 84 Carter (10.1016/j.cell.2019.10.007_bib22) 2012; 30 Hara (10.1016/j.cell.2019.10.007_bib58) 2017; 35 She (10.1016/j.cell.2019.10.007_bib151) 2010; 18 Zhang (10.1016/j.cell.2019.10.007_bib188) 2014; 513 Wang (10.1016/j.cell.2019.10.007_bib175) 2017; 45 Shannon (10.1016/j.cell.2019.10.007_bib150) 2003; 13 Diamond (10.1016/j.cell.2019.10.007_bib36) 2015; 96 Mermel (10.1016/j.cell.2019.10.007_bib103) 2011; 12 Johnson (10.1016/j.cell.2019.10.007_bib72) 2007; 8 Birdsey (10.1016/j.cell.2019.10.007_bib15) 2015; 32 Layer (10.1016/j.cell.2019.10.007_bib84) 2014; 15 Xu (10.1016/j.cell.2019.10.007_bib184) 2017; 33 Hsieh (10.1016/j.cell.2019.10.007_bib64) 2017; 3 Keller (10.1016/j.cell.2019.10.007_bib78) 2002; 74 Anderson (10.1016/j.cell.2019.10.007_bib2) 2017; 31 Yoo (10.1016/j.cell.2019.10.007_bib185) 2014; 10 Zhu (10.1016/j.cell.2019.10.007_bib192) 2017; 121 Bucher (10.1016/j.cell.2019.10.007_bib18) 2008; 98 Ogata (10.1016/j.cell.2019.10.007_bib120) 1999; 27 Huang (10.1016/j.cell.2019.10.007_bib69) 2017; 8 Carles (10.1016/j.cell.2019.10.007_bib21) 2018; 23 Smith (10.1016/j.cell.2019.10.007_bib158) 2018; 128 Ardlie (10.1016/j.cell.2019.10.007_bib194) 2015; 348 Austen (10.1016/j.cell.2019.10.007_bib9) 1998; 17 Ow (10.1016/j.cell.2019.10.007_bib123) 2011; 11 Hsieh (10.1016/j.cell.2019.10.007_bib65) 2018; 36 Robinson (10.1016/j.cell.2019.10.007_bib143) 2017; 548 Chen (10.1016/j.cell.2019.10.007_bib27) 2018; 8 Szolek (10.1016/j.cell.2019.10.007_bib165) 2014; 30 Blanco (10.1016/j.cell.2019.10.007_bib16) 2011; 3 Devlin (10.1016/j.cell.2019.10.007_bib35) 2016; 6 Wen (10.1016/j.cell.2019.10.007_bib178) 2019; 29 Beuselinck (10.1016/j.cell.2019.10.007_bib14) 2015; 21 Liberzon (10.1016/j.cell.2019.10.007_bib89) 2011; 27 Lusis (10.1016/j.cell.2019.10.007_bib96) 2005; 65 Maroto (10.1016/j.cell.2019.10.007_bib97) 2017; 10 Jurtz (10.1016/j.cell.2019.10.007_bib75) 2017; 199 Komili (10.1016/j.cell.2019.10.007_bib79) 2008; 9 Seppä (10.1016/j.cell.2019.10.007_bib149) 1982; 92 Sternberg (10.1016/j.cell.2019.10.007_bib162) 2010; 28 Richman (10.1016/j.cell.2019.10.007_bib140) 2016; 7 Naing (10.1016/j.cell.2019.10.007_bib117) 2018; 34 McDermott (10.1016/j.cell.2019.10.007_bib101) 2018; 24 Matheson (10.1016/j.cell.2019.10.007_bib98) 2016; 37 Frew (10.1016/j.cell.2019.10.007_bib46) 2015; 10 Ubersax (10.1016/j.cell.2019.10.007_bib172) 2007; 8 Ferguson (10.1016/j.cell.2019.10.007_bib43) 2018; 17 Lai (10.1016/j.cell.2019.10.007_bib203) 2016; 44 Lih (10.1016/j.cell.2019.10.007_bib90) 2019 Fisher (10.1016/j.cell.2019.10.007_bib44) 2011; 12 Ricketts (10.1016/j.cell.2019.10.007_bib141) 2018; 23 Mehra (10.1016/j.cell.2019.10.007_bib206) 2016; 6 Wang (10.1016/j.cell.2019.10.007_bib177) 2018; 8 Pierre-Jean (10.1016/j.cell.2019.10.007_bib136) 2015; 16 Guo (10.1016/j.cell.2019.10.007_bib55) 2011; 44 Liluashvili (10.1016/j.cell.2019.10.007_bib91) 2017; 6 Koboldt (10.1016/j.cell.2019.10.007_bib202) 2012; 22 Clark (10.1016/j.cell.2019.10.007_bib29) 2018; 17 Thompson (10.1016/j.cell.2019.10.007_bib166) 2003; 75 Fortin (10.1016/j.cell.2019.10.007_bib45) 2014; 15 Petralia (10.1016/j.cell.2019.10.007_bib134) 2018; 34 Chen (10.1016/j.cell.2019.10.007_bib25) 2016; 14 Mertins (10.1016/j.cell.2019.10.007_bib106) 2018; 13 Kapur (10.1016/j.cell.2019.10.007_bib198) 2013; 14 Petralia (10.1016/j.cell.2019.10.007_bib133) 2016; 15 Wilkerson (10.1016/j.cell.2019.10.007_bib182) 2010; 26 Liao (10.1016/j.cell.2019.10.007_bib88) 2015; 208 Papandreou (10.1016/j.cell.2019.10.007_bib126) 2006; 3 Zhou (10.1016/j.cell.2019.10.007_bib191) 2018; 9 Mertins (10.1016/j.cell.2019.10.007_bib105) 2016; 534 Gordan (10.1016/j.cell.2019.10.007_bib54) 2008; 14 Morris (10.1016/j.cell.2019.10.007_bib113) 2011; 12 Pedregosa (10.1016/j.cell.2019.10.007_bib129) 2011; 12 Lehto (10.1016/j.cell.2019.10.007_bib86) 2003; 1631 Ravaud (10.1016/j.cell.2019.10.007_bib139) 2008; 26 Shen (10.1016/j.cell.2019.10.007_bib152) 2011; 1 Scott (10.1016/j.cell.2019.10.007_bib148) 2009; 459 Kim (10.1016/j.cell.2019.10.007_bib201) 2018; 15 Su (10.1016/j.cell.2019.10.007_bib163) 2010; 26 Benjamini (10.1016/j.cell.2019.10.007_bib13) 1995; 57 Siegel (10.1016/j.cell.2019.10.007_bib156) 2018; 68 Vander Haar (10.1016/j.cell.2019.10.007_bib173) 2007; 9 Motzer (10.1016/j.cell.2019.10.007_bib116) 2018; 378 Zhang (10.1016/j.cell.2019.10.007_bib189) 2014; 24 Kanehisa (10.1016/j.cell.2019.10.007_bib77) 2000; 28 Aran (10.1016/j.cell.2019.10.007_bib5) 2017; 18 Ning (10.1016/j.cell.2019.10.007_bib119) 2012; 11 Tsou (10.1016/j.cell.2019.10.007_bib168) 2015; 12 Cibulskis (10.1016/j.cell.2019.10.007_bib195) 2013; 31 Arai (10.1016/j.cell.2019.10.007_bib4) 2012; 33 Mertins (10.1016/j.cell.2019.10.007_bib104) 2013; 10 Lakins (10.1016/j.cell.2019.10.007_bib83) 2018; 9 Silva (10.1016/j.cell.2019.10.007_bib157) 2016; 5 Chen (10.1016/j.cell.2019.10.007_bib24) 2012; 217 Savitski (10.1016/j.cell.2019.10.007_bib147) 2015; 14 Chen (10.1016/j.cell.2019.10.007_bib23) 2017; 541 Escudier (10.1016/j.cell.2019.10.007_bib41) 2007; 356 Panda (10.1016/j.cell.2019.10.007_bib125) 2018; 3 Ruggles (10.1016/j.cell.2019.10.007_bib145) 2016; 15 Hervouet (10.1016/j.cell.2019.10.007_bib61) 2008; 29 Fortin (10.1016/j.cell.2019.10.007_bib196) 2017; 33 Ross (10.1016/j.cell.2019.10.007_bib144) 2004; 3 Hornbeck (10.1016/j.cell.2019.10.007_bib63) 2015; 43 Petralia (10.1016/j.cell.2019.10.007_bib132) 2015; 31 Ye (10.1016/j.cell.2019.10.007_bib207) 2009; 25 Mehra (10.1016/j.cell.2019.10.007_bib102) 2018; 74 Maksimovic (10.1016/j.cell.2019.10.007_bib204) 2016; 5 Colaprico (10.1016/j.cell.2019.10.007_bib30) 2016; 44 Petrella (10.1016/j.cell.2019.10.007_bib135) 2009; 8 Gordan (10.1016/j.cell.2019.10.007_bib52) 2007; 11 Mgrditchian (10.1016/j.cell.2019.10.007_bib107) 2014; 1 Argentini (10.1016/j.cell.2019.10.007_bib6) 2016; 13 Kong (10.1016/j.cell.2019.10.007_bib80) 2017; 14 Malta (10.1016/j.cell.2019.10.007_bib205) 2018; 173 Davis (10.1016/j.cell.2019.10.007_bib32) 2014; 26 Motzer (10.1016/j.cell.2019.10.007_bib114) 2007; 356 Subramanian (10.1016/j.cell.2019.10.007_bib164) 2005; 102 Deutsch (10.1016/j.cell.2019.10.007_bib34) 2015; 9 Matsushita (10.1016/j.cell.2019.10.007_bib99) 2016; 4 Kim (10.1016/j.cell.2019.10.007_bib200) 2014; 5 Song (10.1016/j.cell.2019.10.007_bib160) 2019; 18 Hsieh (10.1016/j.cell.2019.10.007_bib66) 2018; 244 Edge (10.1016/j.cell.2019.10.007_bib38) 2010 Joshi-Tope (10.1016/j.cell.2019.10.007_bib74) 2005; 33 Antonioli (10.1016/j.cell.2019.10.007_bib3) 2013; 19 Mitchell (10.1016/j.cell.2019.10.007_bib109) 2018; 173 31780818 - Nat Rev Nephrol. 2020 Mar;16(3):133-134. doi: 10.1038/s41581-019-0233-5 31923397 - Cell. 2020 Jan 9;180(1):207. doi: 10.1016/j.cell.2019.12.026 |
| References_xml | – volume: 33 start-page: 1487 year: 2012 end-page: 1493 ident: bib4 article-title: Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas publication-title: Carcinogenesis – volume: 14 start-page: 435 year: 2008 end-page: 446 ident: bib54 article-title: HIF-α effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma publication-title: Cancer Cell – volume: 356 start-page: 115 year: 2007 end-page: 124 ident: bib114 article-title: Sunitinib versus interferon alfa in metastatic renal-cell carcinoma publication-title: N. Engl. J. Med. – volume: 13 start-page: 5293 year: 2014 end-page: 5309 ident: bib138 article-title: Isobaric labeling-based relative quantification in shotgun proteomics publication-title: J. Proteome Res. – volume: 15 start-page: 503 year: 2014 ident: bib45 article-title: Functional normalization of 450k methylation array data improves replication in large cancer studies publication-title: Genome Biol. – volume: 102 start-page: 15545 year: 2005 end-page: 15550 ident: bib164 article-title: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles publication-title: Proc. Natl. Acad. Sci. USA – volume: 14 start-page: 7 year: 2013 ident: bib57 article-title: GSVA: gene set variation analysis for microarray and RNA-seq data publication-title: BMC Bioinformatics – volume: 18 start-page: 51 year: 2018 end-page: 63 ident: bib130 article-title: Ribosome biogenesis in cancer: new players and therapeutic avenues publication-title: Nat. Rev. Cancer – volume: 10 start-page: 263 year: 2015 end-page: 289 ident: bib46 article-title: A clearer view of the molecular complexity of clear cell renal cell carcinoma publication-title: Annu. Rev. Pathol. – volume: 5 start-page: 1542 year: 2016 ident: bib157 article-title: : Analyze cancer genomics and epigenomics data using Bioconductor packages publication-title: F1000Res. – volume: 173 start-page: 581 year: 2018 end-page: 594 ident: bib170 article-title: Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal publication-title: Cell – volume: 5 start-page: 1 year: 2016 end-page: 53 ident: bib204 article-title: A cross-package Bioconductor workflow for analysing methylation array data publication-title: F1000Research – volume: 8 start-page: 118 year: 2007 end-page: 127 ident: bib72 article-title: Adjusting batch effects in microarray expression data using empirical Bayes methods publication-title: Biostatistics – volume: 61 start-page: 8.27.1 year: 2018 end-page: 8.27.26 ident: bib76 article-title: Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE publication-title: Curr. Protoc. Bioinformatics – volume: 28 start-page: 27 year: 2000 end-page: 30 ident: bib77 article-title: KEGG: Kyoto Encyclopedia of Genes and Genomes publication-title: Nucleic Acids Res. – volume: 31 start-page: 311 year: 2017 end-page: 325 ident: bib2 article-title: Obstacles Posed by the Tumor Microenvironment to T cell Activity: A Case for Synergistic Therapies publication-title: Cancer Cell – volume: 52 start-page: 91 year: 2003 end-page: 118 ident: bib111 article-title: Consensus Clustering A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data publication-title: Mach. Learn. – volume: 9 start-page: 948 year: 2018 ident: bib83 article-title: Cancer-associated fibroblasts induce antigen-specific deletion of CD8 publication-title: Nat. Commun. – volume: 8 start-page: 33 year: 2015 ident: bib1 article-title: From big data analysis to personalized medicine for all: challenges and opportunities publication-title: BMC Med. Genomics – volume: 31 start-page: i197 year: 2015 end-page: i205 ident: bib132 article-title: Integrative random forest for gene regulatory network inference publication-title: Bioinformatics – volume: 9 start-page: 1045 year: 2018 ident: bib62 article-title: Benchmarking common quantification strategies for large-scale phosphoproteomics publication-title: Nat. Commun. – volume: 7 start-page: 6379 year: 2016 end-page: 6397 ident: bib95 article-title: PRDX2 and PRDX4 are negative regulators of hypoxia-inducible factors under conditions of prolonged hypoxia publication-title: Oncotarget – volume: 26 start-page: 2285 year: 2008 end-page: 2291 ident: bib139 article-title: Lapatinib versus hormone therapy in patients with advanced renal cell carcinoma: a randomized phase III clinical trial publication-title: J. Clin. Oncol. – volume: 4 start-page: 2612 year: 2013 ident: bib186 article-title: Inferring tumour purity and stromal and immune cell admixture from expression data publication-title: Nat. Commun. – volume: 14 start-page: 2476 year: 2016 end-page: 2489 ident: bib25 article-title: Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma publication-title: Cell Rep. – volume: 13 start-page: 2498 year: 2003 end-page: 2504 ident: bib150 article-title: Cytoscape: a software environment for integrated models of biomolecular interaction networks publication-title: Genome Res. – volume: 14 start-page: 2394 year: 2015 end-page: 2404 ident: bib147 article-title: A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets publication-title: Mol. Cell. Proteomics – volume: 12 start-page: 108 year: 2007 end-page: 113 ident: bib53 article-title: HIF and c-Myc: sibling rivals for control of cancer cell metabolism and proliferation publication-title: Cancer Cell – volume: 7 start-page: 11884 year: 2016 ident: bib140 article-title: Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice publication-title: Nat. Commun. – volume: 15 start-page: 1060 year: 2016 end-page: 1071 ident: bib145 article-title: An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer publication-title: Mol. Cell. Proteomics – volume: 17 start-page: 2205 year: 2018 end-page: 2215 ident: bib29 article-title: Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics publication-title: J. Proteome Res. – volume: 217 start-page: 385 year: 2012 end-page: 393 ident: bib24 article-title: Interferon-γ-induced PD-L1 surface expression on human oral squamous carcinoma via PKD2 signal pathway publication-title: Immunobiology – volume: 14 start-page: 249 year: 2013 end-page: 256 ident: bib7 article-title: MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study publication-title: Lancet Oncol. – volume: 18 start-page: 436 year: 2013 end-page: 445 ident: bib161 article-title: Robust and tissue-independent gender-specific transcript biomarkers publication-title: Biomarkers – volume: 121 start-page: 636 year: 2017 end-page: 649 ident: bib192 article-title: SUMOylation negatively regulates angiogenesis by targeting endothelial NOTCH signaling publication-title: Circ. Res. – volume: 19 start-page: 5435 year: 2000 end-page: 5443 ident: bib81 article-title: Up-regulation of hypoxia-inducible factors HIF-1α and HIF-2α under normoxic conditions in renal carcinoma cells by von Hippel-Lindau tumor suppressor gene loss of function publication-title: Oncogene – volume: 37 start-page: 872 year: 2016 end-page: 881 ident: bib98 article-title: Targeting WEE1 Kinase in Cancer publication-title: Trends Pharmacol. Sci. – volume: 31 start-page: 213 year: 2013 end-page: 219 ident: bib195 article-title: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples publication-title: Nat. Biotechnol. – volume: 15 start-page: R84 year: 2014 ident: bib84 article-title: LUMPY: a probabilistic framework for structural variant discovery publication-title: Genome Biol. – volume: 18 start-page: 39 year: 2010 end-page: 51 ident: bib151 article-title: 4E-BP1 is a key effector of the oncogenic activation of the AKT and ERK signaling pathways that integrates their function in tumors publication-title: Cancer Cell – volume: 17 start-page: 353 year: 2018 end-page: 377 ident: bib43 article-title: Kinase inhibitors: the road ahead publication-title: Nat. Rev. Drug Discov. – volume: 68 start-page: 81 year: 2008 end-page: 88 ident: bib68 article-title: Inhibition of MAPK kinase signaling pathways suppressed renal cell carcinoma growth and angiogenesis in vivo publication-title: Cancer Res. – volume: 21 start-page: 405 year: 2016 end-page: 416 ident: bib159 article-title: One-Class Detection of Cell States in Tumor Subtypes publication-title: Pac. Symp. Biocomput. – volume: 3 start-page: 17009 year: 2017 ident: bib64 article-title: Renal cell carcinoma publication-title: Nat. Rev. Dis. Primers – volume: 84 start-page: 7469 year: 2012 end-page: 7478 ident: bib100 article-title: Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses publication-title: Anal. Chem. – volume: 27 start-page: 29 year: 1999 end-page: 34 ident: bib120 article-title: KEGG: Kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. – volume: 43 start-page: D512 year: 2015 end-page: D520 ident: bib63 article-title: PhosphoSitePlus, 2014: mutations, PTMs and recalibrations publication-title: Nucleic Acids Res. – volume: 459 start-page: 1085 year: 2009 end-page: 1090 ident: bib148 article-title: GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer publication-title: Nature – volume: 30 start-page: 3310 year: 2014 end-page: 3316 ident: bib165 article-title: OptiType: precision HLA typing from next-generation sequencing data publication-title: Bioinformatics – volume: 33 start-page: D428 year: 2005 end-page: D432 ident: bib74 article-title: Reactome: a knowledgebase of biological pathways publication-title: Nucleic Acids Res. – volume: 534 start-page: 55 year: 2016 end-page: 62 ident: bib105 article-title: Proteogenomics connects somatic mutations to signalling in breast cancer publication-title: Nature – volume: 370 start-page: 2103 year: 2007 end-page: 2111 ident: bib42 article-title: Bevacizumab plus interferon alfa-2a for treatment of metastatic renal cell carcinoma: a randomised, double-blind phase III trial publication-title: Lancet – volume: 8 start-page: 14864 year: 2017 ident: bib69 article-title: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts publication-title: Nat. Commun. – volume: 19 start-page: 355 year: 2013 end-page: 367 ident: bib3 article-title: CD39 and CD73 in immunity and inflammation publication-title: Trends Mol. Med. – volume: 33 start-page: 3131 year: 2017 end-page: 3133 ident: bib184 article-title: CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization publication-title: Bioinformatics – volume: 11 start-page: 726 year: 2011 end-page: 734 ident: bib11 article-title: A decade of exploring the cancer epigenome - biological and translational implications publication-title: Nat. Rev. Cancer – volume: 24 start-page: 749 year: 2018 end-page: 757 ident: bib101 article-title: Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma publication-title: Nat. Med. – year: 2010 ident: bib38 article-title: AJCC cancer staging manual – volume: 8 start-page: 1142 year: 2018 end-page: 1155 ident: bib177 article-title: An empirical approach leveraging tumorgrafts to dissect the tumor microenvironment in renal cell carcinoma identifies missing link to prognostic inflammatory factors publication-title: Cancer Discov. – volume: 513 start-page: 382 year: 2014 end-page: 387 ident: bib188 article-title: Proteogenomic characterization of human colon and rectal cancer publication-title: Nature – volume: 65 start-page: 7121 year: 2005 end-page: 7126 ident: bib96 article-title: Integrative genomic analysis identifies NDRG2 as a candidate tumor suppressor gene frequently inactivated in clinically aggressive meningioma publication-title: Cancer Res. – volume: 84 start-page: 7188 year: 2012 end-page: 7194 ident: bib179 article-title: High-resolution enabled TMT 8-plexing publication-title: Anal. Chem. – volume: 30 start-page: 413 year: 2012 end-page: 421 ident: bib22 article-title: Absolute quantification of somatic DNA alterations in human cancer publication-title: Nat. Biotechnol. – volume: 5 start-page: 5277 year: 2014 ident: bib200 article-title: MS-GF+ makes progress towards a universal database search tool for proteomics publication-title: Nat. Commun. – volume: 57 start-page: 289 year: 1995 end-page: 300 ident: bib13 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. Series B Stat. Methodol. – volume: 208 start-page: 206 year: 2015 end-page: 214 ident: bib88 article-title: The roles of chromatin-remodelers and epigenetic modifiers in kidney cancer publication-title: Cancer Genet. – volume: 14 start-page: 159 year: 2013 end-page: 167 ident: bib198 article-title: Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: A retrospective analysis with independent validation publication-title: Lancet Oncol. – volume: 12 start-page: 2825 year: 2011 end-page: 2830 ident: bib129 article-title: Scikit-learn: Machine Learning in Python publication-title: J. Mach. Learn. Res. – volume: 28 start-page: 1061 year: 2010 end-page: 1068 ident: bib162 article-title: Pazopanib in locally advanced or metastatic renal cell carcinoma: results of a randomized phase III trial publication-title: J. Clin. Oncol. – volume: 24 start-page: 2534 year: 2008 end-page: 2536 ident: bib199 article-title: ProteoWizard: Open source software for rapid proteomics tools development publication-title: Bioinformatics – volume: 8 start-page: 530 year: 2007 end-page: 541 ident: bib172 article-title: Mechanisms of specificity in protein phosphorylation publication-title: Nat. Rev. Mol. Cell Biol. – volume: 32 start-page: 82 year: 2015 end-page: 96 ident: bib15 article-title: The endothelial transcription factor ERG promotes vascular stability and growth through Wnt/β-catenin signaling publication-title: Dev. Cell – volume: 11 start-page: 2341 year: 2011 end-page: 2346 ident: bib123 article-title: Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation publication-title: Proteomics – volume: 173 start-page: 338 year: 2018 end-page: 354 ident: bib205 article-title: Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation Article Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation publication-title: Cell – volume: 348 start-page: 648 year: 2015 end-page: 660 ident: bib194 article-title: The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans publication-title: Science – volume: 13 start-page: 1632 year: 2018 end-page: 1661 ident: bib106 article-title: Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry publication-title: Nat. Protoc. – volume: 10 start-page: 4635 year: 2017 end-page: 4643 ident: bib97 article-title: HIF pathway and c-Myc as biomarkers for response to sunitinib in metastatic clear-cell renal cell carcinoma publication-title: OncoTargets Ther. – volume: 9 start-page: 316 year: 2007 end-page: 323 ident: bib173 article-title: Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40 publication-title: Nat. Cell Biol. – volume: 199 start-page: 3360 year: 2017 end-page: 3368 ident: bib75 article-title: NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data publication-title: J. Immunol. – volume: 19 start-page: 460 year: 2013 end-page: 473 ident: bib20 article-title: Multifarious functions of PDGFs and PDGFRs in tumor growth and metastasis publication-title: Trends Mol. Med. – volume: 44 start-page: e71 year: 2016 ident: bib30 article-title: TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data publication-title: Nucleic Acids Res. – volume: 499 start-page: 43 year: 2013 end-page: 49 ident: bib31 article-title: Comprehensive molecular characterization of clear cell renal cell carcinoma publication-title: Nature – year: 2019 ident: bib90 article-title: Omic-Sig: Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions publication-title: bioRxiv – volume: 3 start-page: 1154 year: 2004 end-page: 1169 ident: bib144 article-title: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents publication-title: Mol. Cell. Proteomics – volume: 11 start-page: 335 year: 2007 end-page: 347 ident: bib52 article-title: HIF-2α promotes hypoxic cell proliferation by enhancing c-myc transcriptional activity publication-title: Cancer Cell – volume: 96 start-page: 518 year: 2015 end-page: 526 ident: bib36 article-title: Cytotoxic chemotherapy in the treatment of advanced renal cell carcinoma in the era of targeted therapy publication-title: Crit. Rev. Oncol. Hematol. – volume: 33 start-page: 558 year: 2017 end-page: 560 ident: bib196 article-title: Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi publication-title: Bioinformatics – volume: 98 start-page: 5116 year: 2001 end-page: 5121 ident: bib171 article-title: Significance analysis of microarrays applied to the ionizing radiation response publication-title: Proc. Natl. Acad. Sci. USA – volume: 76 start-page: 1284 year: 2016 end-page: 1296 ident: bib92 article-title: EGFR signaling enhances aerobic glycolysis in triple-negative breast cancer cells to promote tumor growth and immune escape publication-title: Cancer Res. – volume: 166 start-page: 755 year: 2016 end-page: 765 ident: bib190 article-title: Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer publication-title: Cell – volume: 44 start-page: 1 year: 2016 end-page: 11 ident: bib203 article-title: VarDict: A novel and versatile variant caller for next-generation sequencing in cancer research publication-title: Nucleic Acids Res. – volume: 12 start-page: R41 year: 2011 ident: bib103 article-title: GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers publication-title: Genome Biol. – volume: 35 start-page: 363 year: 2017 end-page: 369 ident: bib58 article-title: Expression pattern of immune checkpoint-associated molecules in radical nephrectomy specimens as a prognosticator in patients with metastatic renal cell carcinoma treated with tyrosine kinase inhibitors publication-title: Urol. Oncol. – volume: 34 start-page: i528 year: 2018 end-page: i536 ident: bib134 article-title: A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity publication-title: Bioinformatics – volume: 175 start-page: 998 year: 2018 end-page: 1013.e20 ident: bib146 article-title: Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma publication-title: Cell – volume: 16 start-page: 600 year: 2015 end-page: 615 ident: bib136 article-title: Performance evaluation of DNA copy number segmentation methods publication-title: Brief. Bioinform. – volume: 10 start-page: 634 year: 2013 end-page: 637 ident: bib104 article-title: Integrated proteomic analysis of post-translational modifications by serial enrichment publication-title: Nat. Methods – volume: 173 start-page: 611 year: 2018 end-page: 623 ident: bib109 article-title: Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal publication-title: Cell – volume: 3 start-page: 121522 year: 2018 ident: bib125 article-title: Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma publication-title: JCI Insight – volume: 378 start-page: 1277 year: 2018 end-page: 1290 ident: bib116 article-title: Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma publication-title: N. Engl. J. Med. – volume: 34 start-page: 775 year: 2018 end-page: 791.e3 ident: bib117 article-title: PEGylated IL-10 (Pegilodecakin) Induces Systemic Immune Activation, CD8 publication-title: Cancer Cell – volume: 26 start-page: 319 year: 2014 end-page: 330 ident: bib32 article-title: The somatic genomic landscape of chromophobe renal cell carcinoma publication-title: Cancer Cell – volume: 24 start-page: 331 year: 2014 end-page: 343 ident: bib189 article-title: VGLL4 functions as a new tumor suppressor in lung cancer by negatively regulating the YAP-TEAD transcriptional complex publication-title: Cell Res. – volume: 29 start-page: 1528 year: 2008 end-page: 1537 ident: bib61 article-title: HIF and reactive oxygen species regulate oxidative phosphorylation in cancer publication-title: Carcinogenesis – volume: 12 start-page: 258 year: 2015 end-page: 264 ident: bib168 article-title: DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics publication-title: Nat. Methods – volume: 7 start-page: 2443 year: 2015 end-page: 2458 ident: bib154 article-title: Cancer-associated fibroblasts: Their characteristics and their roles in tumor growth publication-title: Cancers (Basel) – volume: 36 year: 2018 ident: bib65 article-title: Chromosome 3p Loss-Orchestrated VHL, HIF, and Epigenetic Deregulation in Clear Cell Renal Cell Carcinoma publication-title: J. Clin. Oncol. – volume: 548 start-page: 297 year: 2017 end-page: 303 ident: bib143 article-title: Integrative clinical genomics of metastatic cancer publication-title: Nature – year: 2019 ident: bib124 article-title: OmicsX: a web server for integrated OMICS analysis publication-title: bioRxiv – volume: 74 start-page: 483 year: 2018 end-page: 486 ident: bib102 article-title: Somatic Bi-allelic Loss of TSC Genes in Eosinophilic Solid and Cystic Renal Cell Carcinoma publication-title: Eur. Urol. – volume: 18 start-page: 220 year: 2017 ident: bib5 article-title: xCell: digitally portraying the tissue cellular heterogeneity landscape publication-title: Genome Biol. – volume: 17 start-page: 511 year: 1998 end-page: 520 ident: bib9 article-title: YY1 can inhibit c-Myc function through a mechanism requiring DNA binding of YY1 but neither its transactivation domain nor direct interaction with c-Myc publication-title: Oncogene – volume: 244 start-page: 525 year: 2018 end-page: 537 ident: bib66 article-title: Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision publication-title: J. Pathol. – volume: 23 start-page: 313 year: 2018 end-page: 326 ident: bib141 article-title: The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma publication-title: Cell Rep. – volume: 30 start-page: 1002 year: 2016 end-page: 1019 ident: bib48 article-title: Carcinoma-associated fibroblasts: orchestrating the composition of malignancy publication-title: Genes Dev. – volume: 4 start-page: 463 year: 2016 end-page: 471 ident: bib99 article-title: Neoantigen Load, Antigen Presentation Machinery, and Immune Signatures Determine Prognosis in Clear Cell Renal Cell Carcinoma publication-title: Cancer Immunol. Res. – volume: 445 start-page: 776 year: 2007 end-page: 780 ident: bib60 article-title: Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis publication-title: Nature – volume: 13 start-page: 410 year: 2017 end-page: 419 ident: bib180 article-title: Metabolic reprogramming in clear cell renal cell carcinoma publication-title: Nat. Rev. Nephrol. – volume: 541 start-page: 321 year: 2017 end-page: 330 ident: bib23 article-title: Elements of cancer immunity and the cancer-immune set point publication-title: Nature – volume: 8 start-page: 88 year: 2015 ident: bib153 article-title: Role of DNA methylation in renal cell carcinoma publication-title: J. Hematol. Oncol. – volume: 75 start-page: 4646 year: 2003 end-page: 4658 ident: bib118 article-title: A statistical model for identifying proteins by tandem mass spectrometry publication-title: Anal. Chem. – volume: 19 start-page: 1189 year: 2017 end-page: 1201 ident: bib47 article-title: Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression publication-title: Cell Rep. – volume: 1 start-page: 222 year: 2011 end-page: 235 ident: bib152 article-title: Genetic and functional studies implicate HIF1α as a 14q kidney cancer suppressor gene publication-title: Cancer Discov. – volume: 7 start-page: 10975 year: 2016 ident: bib59 article-title: Interphase APC/C-Cdc20 inhibition by cyclin A2-Cdk2 ensures efficient mitotic entry publication-title: Nat. Commun. – volume: 22 start-page: 2445 year: 2016 end-page: 2452 ident: bib82 article-title: Mutations in TSC1, TSC2, and MTOR are associated with response to rapalogs in patients with metastatic renal cell carcinoma publication-title: Clin. Cancer Res. – volume: 6 start-page: 1258 year: 2016 end-page: 1266 ident: bib206 article-title: Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney publication-title: Cancer Discov. – volume: 11 start-page: 2261 year: 2012 end-page: 2271 ident: bib119 article-title: Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data publication-title: J. Proteome Res. – volume: 13 start-page: 964 year: 2016 end-page: 966 ident: bib6 article-title: moFF: a robust and automated approach to extract peptide ion intensities publication-title: Nat. Methods – volume: 6 start-page: 59 year: 2016 end-page: 70 ident: bib35 article-title: Combination therapy targeting ribosome biogenesis and mRNA translation synergistically extends survival in MYC-driven lymphoma publication-title: Cancer Discov. – volume: 20 start-page: 1476 year: 2017 end-page: 1489 ident: bib93 article-title: Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes publication-title: Cell Rep. – volume: 85 start-page: 717 year: 2005 end-page: 736 ident: bib85 article-title: Detecting multiple change-points in the mean of Gaussian process by model selection publication-title: Signal Processing – volume: 26 start-page: 1572 year: 2010 end-page: 1573 ident: bib182 article-title: ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking publication-title: Bioinformatics – volume: 8 start-page: 1156 year: 2018 end-page: 1175 ident: bib27 article-title: CD38-mediated immunosuppression as a mechanism of tumor cell escape from PD-1/PD-l1 blockade publication-title: Cancer Discov. – volume: 26 start-page: 3135 year: 2010 end-page: 3137 ident: bib163 article-title: GLay: community structure analysis of biological networks publication-title: Bioinformatics – volume: 22 start-page: 568 year: 2012 end-page: 576 ident: bib202 article-title: VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing publication-title: Genome Res. – volume: 23 start-page: 1 year: 2018 end-page: 18 ident: bib21 article-title: PKIDB: A curated, annotated and updated database of protein kinase inhibitors in clinical trials publication-title: Molecules – volume: 128 start-page: 4804 year: 2018 end-page: 4820 ident: bib158 article-title: Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma publication-title: J. Clin. Invest. – volume: 45 start-page: W130 year: 2017 end-page: W137 ident: bib175 article-title: WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit publication-title: Nucleic Acids Res. – volume: 2014 start-page: 735292 year: 2014 ident: bib37 article-title: Epigenetic alterations of chromosome 3 revealed by NotI-microarrays in clear cell renal cell carcinoma publication-title: BioMed Res. Int. – volume: 12 start-page: R1 year: 2011 ident: bib44 article-title: A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries publication-title: Genome Biol. – volume: 3 start-page: 187 year: 2006 end-page: 197 ident: bib126 article-title: HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption publication-title: Cell Metab. – volume: 1631 start-page: 1 year: 2003 end-page: 11 ident: bib86 article-title: The OSBP-related proteins: a novel protein family involved in vesicle transport, cellular lipid metabolism, and cell signalling publication-title: Biochim. Biophys. Acta – volume: 92 start-page: 584 year: 1982 end-page: 588 ident: bib149 article-title: Platelet-derived Growth Factor Is Chemotactic for Fibroblasts publication-title: J. Cell Biol. – volume: 20 start-page: 1253 year: 2015 end-page: 1260 ident: bib155 article-title: The Association Between PD-L1 Expression and the Clinical Outcomes to Vascular Endothelial Growth Factor-Targeted Therapy in Patients With Metastatic Clear Cell Renal Cell Carcinoma publication-title: Oncologist – volume: 173 start-page: 595 year: 2018 end-page: 610 ident: bib169 article-title: Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal publication-title: Cell – volume: 35 start-page: 1249 year: 2019 end-page: 1251 ident: bib87 article-title: PDV: an integrative proteomics data viewer publication-title: Bioinformatics – volume: 11 start-page: 13 year: 2016 ident: bib142 article-title: PureCN: copy number calling and SNV classification using targeted short read sequencing publication-title: Source Code Biol. Med. – volume: 29 start-page: 104 year: 2016 end-page: 116 ident: bib56 article-title: An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma publication-title: Cancer Cell – year: 2019 ident: bib67 article-title: OmicsOne: Associate Omics Data with Phenotypes in One-Click publication-title: bioRxiv – volume: 319 start-page: 2350 year: 2013 end-page: 2359 ident: bib28 article-title: Distinct functions for Rap1 signaling in vascular morphogenesis and dysfunction publication-title: Exp. Cell Res. – volume: 4 start-page: 284 year: 1961 ident: bib12 article-title: On the approximation of curves by line segments using dynamic programming publication-title: Commun. ACM – volume: 15 start-page: 743 year: 2016 end-page: 754 ident: bib133 article-title: New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer publication-title: J. Proteome Res. – volume: 21 start-page: 1329 year: 2015 end-page: 1339 ident: bib14 article-title: Molecular subtypes of clear cell renal cell carcinoma are associated with sunitinib response in the metastatic setting publication-title: Clin. Cancer Res. – volume: 8 start-page: 15770 year: 2017 ident: bib10 article-title: MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma publication-title: Nat. Commun. – volume: 3 start-page: 694 year: 2014 ident: bib71 article-title: Tumor grade of clear cell renal cell carcinoma assessed by contrast-enhanced computed tomography publication-title: Springerplus – volume: 15 start-page: 591 year: 2018 end-page: 594 ident: bib201 article-title: Strelka2: fast and accurate calling of germline and somatic variants publication-title: Nat. Methods – volume: 18 start-page: S52 year: 2019 end-page: S65 ident: bib160 article-title: Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis publication-title: Mol. Cell. Proteomics – volume: 8 start-page: 1389 year: 2009 end-page: 1401 ident: bib135 article-title: PTEN suppression of YY1 induces HIF-2α activity in von-Hippel-Lindau-null renal-cell carcinoma publication-title: Cancer Biol. Ther. – volume: 68 start-page: 7 year: 2018 end-page: 30 ident: bib156 article-title: Cancer statistics, 2018 publication-title: CA Cancer J. Clin. – volume: 3 start-page: 4010 year: 2011 end-page: 4023 ident: bib16 article-title: Role of radiation therapy in the management of renal cell cancer publication-title: Cancers (Basel) – volume: 1 start-page: 7 year: 2014 ident: bib107 article-title: Hypoxia: A Key Feature of the Tumor Microenvironment Triggers Several Mechanisms of Evasion from Natural Killer and Cytotoxic T Lymphocytes Surveillance publication-title: J. Immun. Res. – volume: 75 start-page: 1895 year: 2003 end-page: 1904 ident: bib166 article-title: Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS publication-title: Anal. Chem. – volume: 70 start-page: 127 year: 2018 end-page: 137 ident: bib8 article-title: Current and emerging therapies for first-line treatment of metastatic clear cell renal cell carcinoma publication-title: Cancer Treat. Rev. – volume: 46 start-page: 225 year: 2014 end-page: 233 ident: bib50 article-title: Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing publication-title: Nat. Genet. – volume: 42 start-page: 1571 year: 2018 end-page: 1584 ident: bib176 article-title: VSTM2A over-expression is a sensitive and specific biomarker for mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney publication-title: Am. J. Surg. Pathol. – volume: 356 start-page: 2271 year: 2007 end-page: 2281 ident: bib70 article-title: Temsirolimus, interferon alfa, or both for advanced renal-cell carcinoma publication-title: N. Engl. J. Med. – volume: 14 start-page: 513 year: 2017 end-page: 520 ident: bib80 article-title: MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics publication-title: Nat. Methods – volume: 37 start-page: 252 year: 2003 end-page: 260 ident: bib128 article-title: Patterns of aneuploidy in stage IV clear cell renal cell carcinoma revealed by comparative genomic hybridization and spectral karyotyping publication-title: Genes Chromosomes Cancer – volume: 32 start-page: 1220 year: 2016 end-page: 1222 ident: bib26 article-title: Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications publication-title: Bioinformatics – volume: 11 start-page: 1009 year: 2012 end-page: 1017 ident: bib174 article-title: Protein identification using customized protein sequence databases derived from RNA-Seq data publication-title: J. Proteome Res. – volume: 10 start-page: e1003790 year: 2014 ident: bib185 article-title: MODMatcher: multi-omics data matcher for integrative genomic analysis publication-title: PLoS Comput. Biol. – volume: 44 start-page: 17 year: 2011 end-page: 19 ident: bib55 article-title: Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma publication-title: Nat. Genet. – volume: 374 start-page: 135 year: 2016 end-page: 145 ident: bib94 article-title: Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma publication-title: N. Engl. J. Med. – volume: 45 start-page: 849 year: 2013 end-page: 850 ident: bib197 article-title: A clear picture of renal cell carcinoma publication-title: Nat. Genet. – volume: 6 start-page: 1 year: 2017 end-page: 13 ident: bib91 article-title: iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D publication-title: Gigascience – volume: 29 start-page: 485 year: 2019 end-page: 493 ident: bib178 article-title: PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations publication-title: Genome Res. – volume: 12 start-page: 436 year: 2011 ident: bib113 article-title: clusterMaker: a multi-algorithm clustering plugin for Cytoscape publication-title: BMC Bioinformatics – volume: 73 start-page: 1787 year: 2013 end-page: 1799 ident: bib183 article-title: Transcription factor YY1 contributes to tumor growth by stabilizing hypoxia factor HIF-1α in a p53-independent manner publication-title: Cancer Res. – volume: 25 start-page: 2865 year: 2009 end-page: 2871 ident: bib207 article-title: Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads publication-title: Bioinformatics – volume: 9 start-page: 3303 year: 2018 ident: bib191 article-title: SUMOylation of VEGFR2 regulates its intracellular trafficking and pathological angiogenesis publication-title: Nat. Commun. – volume: 12 year: 2008 ident: bib51 article-title: Using CART to Detect Multiple Change Points in the Mean for Large Sample publication-title: Stat. Syst. Biol. – volume: 74 start-page: 5383 year: 2002 end-page: 5392 ident: bib78 article-title: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search publication-title: Anal. Chem. – volume: 9 start-page: 745 year: 2015 end-page: 754 ident: bib34 article-title: Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics publication-title: Proteomics Clin. Appl. – volume: 98 start-page: 523 year: 2008 end-page: 528 ident: bib18 article-title: G2 checkpoint abrogation and checkpoint kinase-1 targeting in the treatment of cancer publication-title: Br. J. Cancer – volume: 27 start-page: 1739 year: 2011 end-page: 1740 ident: bib89 article-title: Molecular signatures database (MSigDB) 3.0 publication-title: Bioinformatics – volume: 9 start-page: 414 year: 2018 ident: bib193 article-title: Alteration of the antitumor immune response by cancer-associated fibroblasts publication-title: Front. Immunol. – volume: 356 start-page: 125 year: 2007 end-page: 134 ident: bib41 article-title: Sorafenib in advanced clear-cell renal-cell carcinoma publication-title: N. Engl. J. Med. – volume: 372 start-page: 449 year: 2008 end-page: 456 ident: bib115 article-title: Efficacy of everolimus in advanced renal cell carcinoma: a double-blind, randomised, placebo-controlled phase III trial publication-title: Lancet – volume: 9 start-page: 38 year: 2008 end-page: 48 ident: bib79 article-title: Coupling and coordination in gene expression processes: a systems biology view publication-title: Nat. Rev. Genet. – volume: 319 start-page: 2350 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib28 article-title: Distinct functions for Rap1 signaling in vascular morphogenesis and dysfunction publication-title: Exp. Cell Res. doi: 10.1016/j.yexcr.2013.07.022 – volume: 12 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib51 article-title: Using CART to Detect Multiple Change Points in the Mean for Large Sample publication-title: Stat. Syst. Biol. – volume: 75 start-page: 1895 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib166 article-title: Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS publication-title: Anal. Chem. doi: 10.1021/ac0262560 – volume: 11 start-page: 726 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib11 article-title: A decade of exploring the cancer epigenome - biological and translational implications publication-title: Nat. Rev. Cancer doi: 10.1038/nrc3130 – volume: 19 start-page: 460 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib20 article-title: Multifarious functions of PDGFs and PDGFRs in tumor growth and metastasis publication-title: Trends Mol. Med. doi: 10.1016/j.molmed.2013.05.002 – volume: 10 start-page: 263 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib46 article-title: A clearer view of the molecular complexity of clear cell renal cell carcinoma publication-title: Annu. Rev. Pathol. doi: 10.1146/annurev-pathol-012414-040306 – volume: 6 start-page: 59 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib35 article-title: Combination therapy targeting ribosome biogenesis and mRNA translation synergistically extends survival in MYC-driven lymphoma publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-14-0673 – volume: 17 start-page: 353 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib43 article-title: Kinase inhibitors: the road ahead publication-title: Nat. Rev. Drug Discov. doi: 10.1038/nrd.2018.21 – volume: 7 start-page: 11884 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib140 article-title: Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice publication-title: Nat. Commun. doi: 10.1038/ncomms11884 – volume: 24 start-page: 749 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib101 article-title: Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma publication-title: Nat. Med. doi: 10.1038/s41591-018-0053-3 – volume: 15 start-page: 1060 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib145 article-title: An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M115.056226 – volume: 10 start-page: e1003790 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib185 article-title: MODMatcher: multi-omics data matcher for integrative genomic analysis publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1003790 – volume: 74 start-page: 483 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib102 article-title: Somatic Bi-allelic Loss of TSC Genes in Eosinophilic Solid and Cystic Renal Cell Carcinoma publication-title: Eur. Urol. doi: 10.1016/j.eururo.2018.06.007 – volume: 8 start-page: 1142 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib177 article-title: An empirical approach leveraging tumorgrafts to dissect the tumor microenvironment in renal cell carcinoma identifies missing link to prognostic inflammatory factors publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-17-1246 – volume: 46 start-page: 225 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib50 article-title: Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing publication-title: Nat. Genet. doi: 10.1038/ng.2891 – volume: 24 start-page: 2534 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib199 article-title: ProteoWizard: Open source software for rapid proteomics tools development publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn323 – volume: 25 start-page: 2865 year: 2009 ident: 10.1016/j.cell.2019.10.007_bib207 article-title: Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp394 – volume: 30 start-page: 1002 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib48 article-title: Carcinoma-associated fibroblasts: orchestrating the composition of malignancy publication-title: Genes Dev. doi: 10.1101/gad.279737.116 – volume: 12 start-page: R1 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib44 article-title: A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries publication-title: Genome Biol. doi: 10.1186/gb-2011-12-1-r1 – volume: 85 start-page: 717 year: 2005 ident: 10.1016/j.cell.2019.10.007_bib85 article-title: Detecting multiple change-points in the mean of Gaussian process by model selection publication-title: Signal Processing doi: 10.1016/j.sigpro.2004.11.012 – volume: 20 start-page: 1476 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib93 article-title: Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes publication-title: Cell Rep. doi: 10.1016/j.celrep.2017.07.043 – volume: 8 start-page: 1389 year: 2009 ident: 10.1016/j.cell.2019.10.007_bib135 article-title: PTEN suppression of YY1 induces HIF-2α activity in von-Hippel-Lindau-null renal-cell carcinoma publication-title: Cancer Biol. Ther. doi: 10.4161/cbt.8.14.8880 – volume: 9 start-page: 316 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib173 article-title: Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40 publication-title: Nat. Cell Biol. doi: 10.1038/ncb1547 – year: 2019 ident: 10.1016/j.cell.2019.10.007_bib67 article-title: OmicsOne: Associate Omics Data with Phenotypes in One-Click publication-title: bioRxiv – volume: 199 start-page: 3360 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib75 article-title: NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data publication-title: J. Immunol. doi: 10.4049/jimmunol.1700893 – volume: 32 start-page: 82 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib15 article-title: The endothelial transcription factor ERG promotes vascular stability and growth through Wnt/β-catenin signaling publication-title: Dev. Cell doi: 10.1016/j.devcel.2014.11.016 – volume: 36 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib65 article-title: Chromosome 3p Loss-Orchestrated VHL, HIF, and Epigenetic Deregulation in Clear Cell Renal Cell Carcinoma publication-title: J. Clin. Oncol. doi: 10.1200/JCO.2018.79.2549 – volume: 14 start-page: 513 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib80 article-title: MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics publication-title: Nat. Methods doi: 10.1038/nmeth.4256 – volume: 18 start-page: 51 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib130 article-title: Ribosome biogenesis in cancer: new players and therapeutic avenues publication-title: Nat. Rev. Cancer doi: 10.1038/nrc.2017.104 – volume: 21 start-page: 1329 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib14 article-title: Molecular subtypes of clear cell renal cell carcinoma are associated with sunitinib response in the metastatic setting publication-title: Clin. Cancer Res. doi: 10.1158/1078-0432.CCR-14-1128 – volume: 9 start-page: 414 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib193 article-title: Alteration of the antitumor immune response by cancer-associated fibroblasts publication-title: Front. Immunol. doi: 10.3389/fimmu.2018.00414 – volume: 217 start-page: 385 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib24 article-title: Interferon-γ-induced PD-L1 surface expression on human oral squamous carcinoma via PKD2 signal pathway publication-title: Immunobiology doi: 10.1016/j.imbio.2011.10.016 – volume: 374 start-page: 135 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib94 article-title: Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1505917 – volume: 18 start-page: 436 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib161 article-title: Robust and tissue-independent gender-specific transcript biomarkers publication-title: Biomarkers doi: 10.3109/1354750X.2013.811538 – volume: 166 start-page: 755 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib190 article-title: Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer publication-title: Cell doi: 10.1016/j.cell.2016.05.069 – volume: 31 start-page: 311 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib2 article-title: Obstacles Posed by the Tumor Microenvironment to T cell Activity: A Case for Synergistic Therapies publication-title: Cancer Cell doi: 10.1016/j.ccell.2017.02.008 – volume: 499 start-page: 43 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib31 article-title: Comprehensive molecular characterization of clear cell renal cell carcinoma publication-title: Nature doi: 10.1038/nature12222 – volume: 244 start-page: 525 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib66 article-title: Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision publication-title: J. Pathol. doi: 10.1002/path.5022 – volume: 8 start-page: 88 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib153 article-title: Role of DNA methylation in renal cell carcinoma publication-title: J. Hematol. Oncol. doi: 10.1186/s13045-015-0180-y – volume: 37 start-page: 872 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib98 article-title: Targeting WEE1 Kinase in Cancer publication-title: Trends Pharmacol. Sci. doi: 10.1016/j.tips.2016.06.006 – volume: 19 start-page: 355 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib3 article-title: CD39 and CD73 in immunity and inflammation publication-title: Trends Mol. Med. doi: 10.1016/j.molmed.2013.03.005 – volume: 3 start-page: 4010 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib16 article-title: Role of radiation therapy in the management of renal cell cancer publication-title: Cancers (Basel) doi: 10.3390/cancers3044010 – volume: 35 start-page: 1249 year: 2019 ident: 10.1016/j.cell.2019.10.007_bib87 article-title: PDV: an integrative proteomics data viewer publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty770 – volume: 173 start-page: 581 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib170 article-title: Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal publication-title: Cell doi: 10.1016/j.cell.2018.03.057 – volume: 57 start-page: 289 year: 1995 ident: 10.1016/j.cell.2019.10.007_bib13 article-title: Controlling the false discovery rate: a practical and powerful approach to multiple testing publication-title: J. R. Stat. Soc. Series B Stat. Methodol. doi: 10.1111/j.2517-6161.1995.tb02031.x – volume: 7 start-page: 6379 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib95 article-title: PRDX2 and PRDX4 are negative regulators of hypoxia-inducible factors under conditions of prolonged hypoxia publication-title: Oncotarget doi: 10.18632/oncotarget.7142 – volume: 370 start-page: 2103 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib42 article-title: Bevacizumab plus interferon alfa-2a for treatment of metastatic renal cell carcinoma: a randomised, double-blind phase III trial publication-title: Lancet doi: 10.1016/S0140-6736(07)61904-7 – volume: 356 start-page: 2271 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib70 article-title: Temsirolimus, interferon alfa, or both for advanced renal-cell carcinoma publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa066838 – volume: 45 start-page: 849 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib197 article-title: A clear picture of renal cell carcinoma publication-title: Nat. Genet. doi: 10.1038/ng.2708 – volume: 128 start-page: 4804 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib158 article-title: Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma publication-title: J. Clin. Invest. doi: 10.1172/JCI121476 – volume: 21 start-page: 405 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib159 article-title: One-Class Detection of Cell States in Tumor Subtypes publication-title: Pac. Symp. Biocomput. – volume: 19 start-page: 5435 year: 2000 ident: 10.1016/j.cell.2019.10.007_bib81 article-title: Up-regulation of hypoxia-inducible factors HIF-1α and HIF-2α under normoxic conditions in renal carcinoma cells by von Hippel-Lindau tumor suppressor gene loss of function publication-title: Oncogene doi: 10.1038/sj.onc.1203938 – volume: 14 start-page: 159 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib198 article-title: Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: A retrospective analysis with independent validation publication-title: Lancet Oncol. doi: 10.1016/S1470-2045(12)70584-3 – volume: 28 start-page: 1061 year: 2010 ident: 10.1016/j.cell.2019.10.007_bib162 article-title: Pazopanib in locally advanced or metastatic renal cell carcinoma: results of a randomized phase III trial publication-title: J. Clin. Oncol. doi: 10.1200/JCO.2009.23.9764 – volume: 13 start-page: 964 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib6 article-title: moFF: a robust and automated approach to extract peptide ion intensities publication-title: Nat. Methods doi: 10.1038/nmeth.4075 – volume: 37 start-page: 252 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib128 article-title: Patterns of aneuploidy in stage IV clear cell renal cell carcinoma revealed by comparative genomic hybridization and spectral karyotyping publication-title: Genes Chromosomes Cancer doi: 10.1002/gcc.10209 – volume: 15 start-page: 743 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib133 article-title: New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer publication-title: J. Proteome Res. doi: 10.1021/acs.jproteome.5b00925 – year: 2010 ident: 10.1016/j.cell.2019.10.007_bib38 – volume: 11 start-page: 2341 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib123 article-title: Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation publication-title: Proteomics doi: 10.1002/pmic.201000752 – volume: 173 start-page: 595 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib169 article-title: Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal publication-title: Cell doi: 10.1016/j.cell.2018.03.043 – volume: 31 start-page: 213 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib195 article-title: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2514 – volume: 28 start-page: 27 year: 2000 ident: 10.1016/j.cell.2019.10.007_bib77 article-title: KEGG: Kyoto Encyclopedia of Genes and Genomes publication-title: Nucleic Acids Res. doi: 10.1093/nar/28.1.27 – volume: 22 start-page: 568 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib202 article-title: VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing publication-title: Genome Res. doi: 10.1101/gr.129684.111 – volume: 378 start-page: 1277 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib116 article-title: Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa1712126 – volume: 33 start-page: 3131 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib184 article-title: CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx378 – volume: 14 start-page: 2476 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib25 article-title: Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma publication-title: Cell Rep. doi: 10.1016/j.celrep.2016.02.024 – volume: 12 start-page: 108 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib53 article-title: HIF and c-Myc: sibling rivals for control of cancer cell metabolism and proliferation publication-title: Cancer Cell doi: 10.1016/j.ccr.2007.07.006 – volume: 6 start-page: 1 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib91 article-title: iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D publication-title: Gigascience doi: 10.1093/gigascience/gix054 – volume: 68 start-page: 7 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib156 article-title: Cancer statistics, 2018 publication-title: CA Cancer J. Clin. doi: 10.3322/caac.21442 – volume: 29 start-page: 485 year: 2019 ident: 10.1016/j.cell.2019.10.007_bib178 article-title: PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations publication-title: Genome Res. doi: 10.1101/gr.235028.118 – volume: 3 start-page: 694 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib71 article-title: Tumor grade of clear cell renal cell carcinoma assessed by contrast-enhanced computed tomography publication-title: Springerplus doi: 10.1186/2193-1801-3-694 – volume: 26 start-page: 3135 year: 2010 ident: 10.1016/j.cell.2019.10.007_bib163 article-title: GLay: community structure analysis of biological networks publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq596 – volume: 8 start-page: 15770 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib10 article-title: MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma publication-title: Nat. Commun. doi: 10.1038/ncomms15770 – volume: 1631 start-page: 1 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib86 article-title: The OSBP-related proteins: a novel protein family involved in vesicle transport, cellular lipid metabolism, and cell signalling publication-title: Biochim. Biophys. Acta doi: 10.1016/S1388-1981(02)00364-5 – volume: 45 start-page: W130 issue: W1 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib175 article-title: WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkx356 – volume: 3 start-page: 121522 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib125 article-title: Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma publication-title: JCI Insight doi: 10.1172/jci.insight.121522 – volume: 44 start-page: 17 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib55 article-title: Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma publication-title: Nat. Genet. doi: 10.1038/ng.1014 – volume: 27 start-page: 29 year: 1999 ident: 10.1016/j.cell.2019.10.007_bib120 article-title: KEGG: Kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res. doi: 10.1093/nar/27.1.29 – volume: 35 start-page: 363 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib58 article-title: Expression pattern of immune checkpoint-associated molecules in radical nephrectomy specimens as a prognosticator in patients with metastatic renal cell carcinoma treated with tyrosine kinase inhibitors publication-title: Urol. Oncol. doi: 10.1016/j.urolonc.2017.01.002 – year: 2019 ident: 10.1016/j.cell.2019.10.007_bib90 article-title: Omic-Sig: Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions publication-title: bioRxiv – volume: 23 start-page: 1 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib21 article-title: PKIDB: A curated, annotated and updated database of protein kinase inhibitors in clinical trials publication-title: Molecules doi: 10.3390/molecules23040908 – volume: 4 start-page: 284 year: 1961 ident: 10.1016/j.cell.2019.10.007_bib12 article-title: On the approximation of curves by line segments using dynamic programming publication-title: Commun. ACM doi: 10.1145/366573.366611 – volume: 102 start-page: 15545 year: 2005 ident: 10.1016/j.cell.2019.10.007_bib164 article-title: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0506580102 – volume: 15 start-page: 503 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib45 article-title: Functional normalization of 450k methylation array data improves replication in large cancer studies publication-title: Genome Biol. doi: 10.1186/s13059-014-0503-2 – volume: 73 start-page: 1787 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib183 article-title: Transcription factor YY1 contributes to tumor growth by stabilizing hypoxia factor HIF-1α in a p53-independent manner publication-title: Cancer Res. doi: 10.1158/0008-5472.CAN-12-0366 – volume: 534 start-page: 55 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib105 article-title: Proteogenomics connects somatic mutations to signalling in breast cancer publication-title: Nature doi: 10.1038/nature18003 – volume: 31 start-page: i197 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib132 article-title: Integrative random forest for gene regulatory network inference publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv268 – volume: 98 start-page: 5116 year: 2001 ident: 10.1016/j.cell.2019.10.007_bib171 article-title: Significance analysis of microarrays applied to the ionizing radiation response publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.091062498 – volume: 12 start-page: 258 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib168 article-title: DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics publication-title: Nat. Methods doi: 10.1038/nmeth.3255 – volume: 96 start-page: 518 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib36 article-title: Cytotoxic chemotherapy in the treatment of advanced renal cell carcinoma in the era of targeted therapy publication-title: Crit. Rev. Oncol. Hematol. doi: 10.1016/j.critrevonc.2015.08.007 – volume: 84 start-page: 7188 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib179 article-title: High-resolution enabled TMT 8-plexing publication-title: Anal. Chem. doi: 10.1021/ac301553x – volume: 14 start-page: 2394 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib147 article-title: A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M114.046995 – volume: 26 start-page: 2285 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib139 article-title: Lapatinib versus hormone therapy in patients with advanced renal cell carcinoma: a randomized phase III clinical trial publication-title: J. Clin. Oncol. doi: 10.1200/JCO.2007.14.5029 – volume: 30 start-page: 413 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib22 article-title: Absolute quantification of somatic DNA alterations in human cancer publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2203 – volume: 43 start-page: D512 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib63 article-title: PhosphoSitePlus, 2014: mutations, PTMs and recalibrations publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku1267 – volume: 13 start-page: 2498 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib150 article-title: Cytoscape: a software environment for integrated models of biomolecular interaction networks publication-title: Genome Res. doi: 10.1101/gr.1239303 – volume: 30 start-page: 3310 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib165 article-title: OptiType: precision HLA typing from next-generation sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu548 – volume: 121 start-page: 636 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib192 article-title: SUMOylation negatively regulates angiogenesis by targeting endothelial NOTCH signaling publication-title: Circ. Res. doi: 10.1161/CIRCRESAHA.117.310696 – volume: 173 start-page: 338 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib205 article-title: Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation Article Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation publication-title: Cell doi: 10.1016/j.cell.2018.03.034 – volume: 14 start-page: 435 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib54 article-title: HIF-α effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma publication-title: Cancer Cell doi: 10.1016/j.ccr.2008.10.016 – volume: 74 start-page: 5383 year: 2002 ident: 10.1016/j.cell.2019.10.007_bib78 article-title: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search publication-title: Anal. Chem. doi: 10.1021/ac025747h – volume: 16 start-page: 600 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib136 article-title: Performance evaluation of DNA copy number segmentation methods publication-title: Brief. Bioinform. doi: 10.1093/bib/bbu026 – volume: 27 start-page: 1739 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib89 article-title: Molecular signatures database (MSigDB) 3.0 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr260 – volume: 356 start-page: 115 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib114 article-title: Sunitinib versus interferon alfa in metastatic renal-cell carcinoma publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa065044 – volume: 1 start-page: 7 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib107 article-title: Hypoxia: A Key Feature of the Tumor Microenvironment Triggers Several Mechanisms of Evasion from Natural Killer and Cytotoxic T Lymphocytes Surveillance publication-title: J. Immun. Res. – volume: 92 start-page: 584 year: 1982 ident: 10.1016/j.cell.2019.10.007_bib149 article-title: Platelet-derived Growth Factor Is Chemotactic for Fibroblasts publication-title: J. Cell Biol. doi: 10.1083/jcb.92.2.584 – volume: 18 start-page: 220 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib5 article-title: xCell: digitally portraying the tissue cellular heterogeneity landscape publication-title: Genome Biol. doi: 10.1186/s13059-017-1349-1 – volume: 29 start-page: 104 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib56 article-title: An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma publication-title: Cancer Cell doi: 10.1016/j.ccell.2015.12.004 – volume: 32 start-page: 1220 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib26 article-title: Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv710 – volume: 7 start-page: 10975 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib59 article-title: Interphase APC/C-Cdc20 inhibition by cyclin A2-Cdk2 ensures efficient mitotic entry publication-title: Nat. Commun. doi: 10.1038/ncomms10975 – volume: 8 start-page: 530 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib172 article-title: Mechanisms of specificity in protein phosphorylation publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm2203 – volume: 9 start-page: 3303 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib191 article-title: SUMOylation of VEGFR2 regulates its intracellular trafficking and pathological angiogenesis publication-title: Nat. Commun. doi: 10.1038/s41467-018-05812-2 – volume: 44 start-page: e71 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib30 article-title: TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkv1507 – volume: 14 start-page: 7 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib57 article-title: GSVA: gene set variation analysis for microarray and RNA-seq data publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-7 – volume: 11 start-page: 13 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib142 article-title: PureCN: copy number calling and SNV classification using targeted short read sequencing publication-title: Source Code Biol. Med. doi: 10.1186/s13029-016-0060-z – volume: 20 start-page: 1253 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib155 article-title: The Association Between PD-L1 Expression and the Clinical Outcomes to Vascular Endothelial Growth Factor-Targeted Therapy in Patients With Metastatic Clear Cell Renal Cell Carcinoma publication-title: Oncologist doi: 10.1634/theoncologist.2015-0151 – volume: 513 start-page: 382 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib188 article-title: Proteogenomic characterization of human colon and rectal cancer publication-title: Nature doi: 10.1038/nature13438 – volume: 348 start-page: 648 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib194 article-title: The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans publication-title: Science doi: 10.1126/science.1262110 – volume: 4 start-page: 2612 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib186 article-title: Inferring tumour purity and stromal and immune cell admixture from expression data publication-title: Nat. Commun. doi: 10.1038/ncomms3612 – volume: 34 start-page: i528 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib134 article-title: A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty280 – volume: 23 start-page: 313 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib141 article-title: The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma publication-title: Cell Rep. doi: 10.1016/j.celrep.2018.03.075 – volume: 8 start-page: 33 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib1 article-title: From big data analysis to personalized medicine for all: challenges and opportunities publication-title: BMC Med. Genomics doi: 10.1186/s12920-015-0108-y – volume: 8 start-page: 14864 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib69 article-title: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts publication-title: Nat. Commun. doi: 10.1038/ncomms14864 – volume: 11 start-page: 2261 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib119 article-title: Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data publication-title: J. Proteome Res. doi: 10.1021/pr201052x – volume: 459 start-page: 1085 year: 2009 ident: 10.1016/j.cell.2019.10.007_bib148 article-title: GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer publication-title: Nature doi: 10.1038/nature08109 – volume: 9 start-page: 1045 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib62 article-title: Benchmarking common quantification strategies for large-scale phosphoproteomics publication-title: Nat. Commun. doi: 10.1038/s41467-018-03309-6 – volume: 12 start-page: 436 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib113 article-title: clusterMaker: a multi-algorithm clustering plugin for Cytoscape publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-436 – volume: 12 start-page: 2825 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib129 article-title: Scikit-learn: Machine Learning in Python publication-title: J. Mach. Learn. Res. – volume: 208 start-page: 206 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib88 article-title: The roles of chromatin-remodelers and epigenetic modifiers in kidney cancer publication-title: Cancer Genet. doi: 10.1016/j.cancergen.2015.02.008 – volume: 15 start-page: R84 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib84 article-title: LUMPY: a probabilistic framework for structural variant discovery publication-title: Genome Biol. doi: 10.1186/gb-2014-15-6-r84 – volume: 75 start-page: 4646 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib118 article-title: A statistical model for identifying proteins by tandem mass spectrometry publication-title: Anal. Chem. doi: 10.1021/ac0341261 – volume: 17 start-page: 2205 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib29 article-title: Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics publication-title: J. Proteome Res. doi: 10.1021/acs.jproteome.8b00165 – volume: 3 start-page: 187 year: 2006 ident: 10.1016/j.cell.2019.10.007_bib126 article-title: HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption publication-title: Cell Metab. doi: 10.1016/j.cmet.2006.01.012 – volume: 13 start-page: 1632 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib106 article-title: Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry publication-title: Nat. Protoc. doi: 10.1038/s41596-018-0006-9 – volume: 15 start-page: 591 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib201 article-title: Strelka2: fast and accurate calling of germline and somatic variants publication-title: Nat. Methods doi: 10.1038/s41592-018-0051-x – volume: 29 start-page: 1528 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib61 article-title: HIF and reactive oxygen species regulate oxidative phosphorylation in cancer publication-title: Carcinogenesis doi: 10.1093/carcin/bgn125 – volume: 1 start-page: 222 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib152 article-title: Genetic and functional studies implicate HIF1α as a 14q kidney cancer suppressor gene publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-11-0098 – volume: 11 start-page: 335 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib52 article-title: HIF-2α promotes hypoxic cell proliferation by enhancing c-myc transcriptional activity publication-title: Cancer Cell doi: 10.1016/j.ccr.2007.02.006 – volume: 24 start-page: 331 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib189 article-title: VGLL4 functions as a new tumor suppressor in lung cancer by negatively regulating the YAP-TEAD transcriptional complex publication-title: Cell Res. doi: 10.1038/cr.2014.10 – volume: 68 start-page: 81 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib68 article-title: Inhibition of MAPK kinase signaling pathways suppressed renal cell carcinoma growth and angiogenesis in vivo publication-title: Cancer Res. doi: 10.1158/0008-5472.CAN-07-5311 – volume: 22 start-page: 2445 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib82 article-title: Mutations in TSC1, TSC2, and MTOR are associated with response to rapalogs in patients with metastatic renal cell carcinoma publication-title: Clin. Cancer Res. doi: 10.1158/1078-0432.CCR-15-2631 – volume: 175 start-page: 998 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib146 article-title: Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma publication-title: Cell doi: 10.1016/j.cell.2018.10.038 – volume: 173 start-page: 611 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib109 article-title: Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal publication-title: Cell doi: 10.1016/j.cell.2018.02.020 – volume: 3 start-page: 17009 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib64 article-title: Renal cell carcinoma publication-title: Nat. Rev. Dis. Primers doi: 10.1038/nrdp.2017.9 – volume: 9 start-page: 948 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib83 article-title: Cancer-associated fibroblasts induce antigen-specific deletion of CD8 + T Cells to protect tumour cells publication-title: Nat. Commun. doi: 10.1038/s41467-018-03347-0 – volume: 65 start-page: 7121 year: 2005 ident: 10.1016/j.cell.2019.10.007_bib96 article-title: Integrative genomic analysis identifies NDRG2 as a candidate tumor suppressor gene frequently inactivated in clinically aggressive meningioma publication-title: Cancer Res. doi: 10.1158/0008-5472.CAN-05-0043 – volume: 5 start-page: 1542 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib157 article-title: TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages publication-title: F1000Res. doi: 10.12688/f1000research.8923.1 – volume: 33 start-page: D428 year: 2005 ident: 10.1016/j.cell.2019.10.007_bib74 article-title: Reactome: a knowledgebase of biological pathways publication-title: Nucleic Acids Res. doi: 10.1093/nar/gki072 – volume: 8 start-page: 118 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib72 article-title: Adjusting batch effects in microarray expression data using empirical Bayes methods publication-title: Biostatistics doi: 10.1093/biostatistics/kxj037 – year: 2019 ident: 10.1016/j.cell.2019.10.007_bib124 article-title: OmicsX: a web server for integrated OMICS analysis publication-title: bioRxiv – volume: 5 start-page: 5277 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib200 article-title: MS-GF+ makes progress towards a universal database search tool for proteomics publication-title: Nat. Commun. doi: 10.1038/ncomms6277 – volume: 7 start-page: 2443 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib154 article-title: Cancer-associated fibroblasts: Their characteristics and their roles in tumor growth publication-title: Cancers (Basel) doi: 10.3390/cancers7040902 – volume: 12 start-page: R41 year: 2011 ident: 10.1016/j.cell.2019.10.007_bib103 article-title: GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers publication-title: Genome Biol. doi: 10.1186/gb-2011-12-4-r41 – volume: 61 start-page: 8.27.1 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib76 article-title: Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE publication-title: Curr. Protoc. Bioinformatics doi: 10.1002/cpbi.47 – volume: 52 start-page: 91 year: 2003 ident: 10.1016/j.cell.2019.10.007_bib111 article-title: Consensus Clustering A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data publication-title: Mach. Learn. doi: 10.1023/A:1023949509487 – volume: 5 start-page: 1 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib204 article-title: A cross-package Bioconductor workflow for analysing methylation array data publication-title: F1000Research doi: 10.12688/f1000research.8839.2 – volume: 17 start-page: 511 year: 1998 ident: 10.1016/j.cell.2019.10.007_bib9 article-title: YY1 can inhibit c-Myc function through a mechanism requiring DNA binding of YY1 but neither its transactivation domain nor direct interaction with c-Myc publication-title: Oncogene doi: 10.1038/sj.onc.1201968 – volume: 2014 start-page: 735292 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib37 article-title: Epigenetic alterations of chromosome 3 revealed by NotI-microarrays in clear cell renal cell carcinoma publication-title: BioMed Res. Int. doi: 10.1155/2014/735292 – volume: 548 start-page: 297 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib143 article-title: Integrative clinical genomics of metastatic cancer publication-title: Nature doi: 10.1038/nature23306 – volume: 3 start-page: 1154 year: 2004 ident: 10.1016/j.cell.2019.10.007_bib144 article-title: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.M400129-MCP200 – volume: 541 start-page: 321 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib23 article-title: Elements of cancer immunity and the cancer-immune set point publication-title: Nature doi: 10.1038/nature21349 – volume: 9 start-page: 745 year: 2015 ident: 10.1016/j.cell.2019.10.007_bib34 article-title: Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics publication-title: Proteomics Clin. Appl. doi: 10.1002/prca.201400164 – volume: 13 start-page: 410 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib180 article-title: Metabolic reprogramming in clear cell renal cell carcinoma publication-title: Nat. Rev. Nephrol. doi: 10.1038/nrneph.2017.59 – volume: 34 start-page: 775 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib117 article-title: PEGylated IL-10 (Pegilodecakin) Induces Systemic Immune Activation, CD8+ T Cell Invigoration and Polyclonal T Cell Expansion in Cancer Patients publication-title: Cancer Cell doi: 10.1016/j.ccell.2018.10.007 – volume: 6 start-page: 1258 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib206 article-title: Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-16-0267 – volume: 18 start-page: 39 year: 2010 ident: 10.1016/j.cell.2019.10.007_bib151 article-title: 4E-BP1 is a key effector of the oncogenic activation of the AKT and ERK signaling pathways that integrates their function in tumors publication-title: Cancer Cell doi: 10.1016/j.ccr.2010.05.023 – volume: 42 start-page: 1571 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib176 article-title: VSTM2A over-expression is a sensitive and specific biomarker for mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney publication-title: Am. J. Surg. Pathol. doi: 10.1097/PAS.0000000000001150 – volume: 76 start-page: 1284 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib92 article-title: EGFR signaling enhances aerobic glycolysis in triple-negative breast cancer cells to promote tumor growth and immune escape publication-title: Cancer Res. doi: 10.1158/0008-5472.CAN-15-2478 – volume: 26 start-page: 319 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib32 article-title: The somatic genomic landscape of chromophobe renal cell carcinoma publication-title: Cancer Cell doi: 10.1016/j.ccr.2014.07.014 – volume: 9 start-page: 38 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib79 article-title: Coupling and coordination in gene expression processes: a systems biology view publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2223 – volume: 84 start-page: 7469 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib100 article-title: Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses publication-title: Anal. Chem. doi: 10.1021/ac301572t – volume: 33 start-page: 558 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib196 article-title: Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw691 – volume: 26 start-page: 1572 year: 2010 ident: 10.1016/j.cell.2019.10.007_bib182 article-title: ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq170 – volume: 445 start-page: 776 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib60 article-title: Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis publication-title: Nature doi: 10.1038/nature05571 – volume: 33 start-page: 1487 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib4 article-title: Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas publication-title: Carcinogenesis doi: 10.1093/carcin/bgs177 – volume: 98 start-page: 523 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib18 article-title: G2 checkpoint abrogation and checkpoint kinase-1 targeting in the treatment of cancer publication-title: Br. J. Cancer doi: 10.1038/sj.bjc.6604208 – volume: 10 start-page: 634 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib104 article-title: Integrated proteomic analysis of post-translational modifications by serial enrichment publication-title: Nat. Methods doi: 10.1038/nmeth.2518 – volume: 10 start-page: 4635 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib97 article-title: HIF pathway and c-Myc as biomarkers for response to sunitinib in metastatic clear-cell renal cell carcinoma publication-title: OncoTargets Ther. doi: 10.2147/OTT.S137677 – volume: 70 start-page: 127 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib8 article-title: Current and emerging therapies for first-line treatment of metastatic clear cell renal cell carcinoma publication-title: Cancer Treat. Rev. doi: 10.1016/j.ctrv.2018.07.009 – volume: 19 start-page: 1189 year: 2017 ident: 10.1016/j.cell.2019.10.007_bib47 article-title: Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression publication-title: Cell Rep. doi: 10.1016/j.celrep.2017.04.031 – volume: 8 start-page: 1156 year: 2018 ident: 10.1016/j.cell.2019.10.007_bib27 article-title: CD38-mediated immunosuppression as a mechanism of tumor cell escape from PD-1/PD-l1 blockade publication-title: Cancer Discov. doi: 10.1158/2159-8290.CD-17-1033 – volume: 14 start-page: 249 year: 2013 ident: 10.1016/j.cell.2019.10.007_bib7 article-title: MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study publication-title: Lancet Oncol. doi: 10.1016/S1470-2045(13)70024-X – volume: 4 start-page: 463 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib99 article-title: Neoantigen Load, Antigen Presentation Machinery, and Immune Signatures Determine Prognosis in Clear Cell Renal Cell Carcinoma publication-title: Cancer Immunol. Res. doi: 10.1158/2326-6066.CIR-15-0225 – volume: 356 start-page: 125 year: 2007 ident: 10.1016/j.cell.2019.10.007_bib41 article-title: Sorafenib in advanced clear-cell renal-cell carcinoma publication-title: N. Engl. J. Med. doi: 10.1056/NEJMoa060655 – volume: 372 start-page: 449 year: 2008 ident: 10.1016/j.cell.2019.10.007_bib115 article-title: Efficacy of everolimus in advanced renal cell carcinoma: a double-blind, randomised, placebo-controlled phase III trial publication-title: Lancet doi: 10.1016/S0140-6736(08)61039-9 – volume: 13 start-page: 5293 year: 2014 ident: 10.1016/j.cell.2019.10.007_bib138 article-title: Isobaric labeling-based relative quantification in shotgun proteomics publication-title: J. Proteome Res. doi: 10.1021/pr500880b – volume: 11 start-page: 1009 year: 2012 ident: 10.1016/j.cell.2019.10.007_bib174 article-title: Protein identification using customized protein sequence databases derived from RNA-Seq data publication-title: J. Proteome Res. doi: 10.1021/pr200766z – volume: 44 start-page: 1 year: 2016 ident: 10.1016/j.cell.2019.10.007_bib203 article-title: VarDict: A novel and versatile variant caller for next-generation sequencing in cancer research publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw227 – volume: 18 start-page: S52 issue: Suppl 1 year: 2019 ident: 10.1016/j.cell.2019.10.007_bib160 article-title: Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis publication-title: Mol. Cell. Proteomics doi: 10.1074/mcp.RA118.001220 – reference: 31923397 - Cell. 2020 Jan 9;180(1):207. doi: 10.1016/j.cell.2019.12.026 – reference: 31780818 - Nat Rev Nephrol. 2020 Mar;16(3):133-134. doi: 10.1038/s41581-019-0233-5 |
| SSID | ssj0008555 |
| Score | 2.7075384 |
| Snippet | To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic,... |
| SourceID | pubmedcentral proquest pubmed crossref elsevier |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 964 |
| SubjectTerms | Adult Aged Aged, 80 and over Biomarkers, Tumor - genetics Biomarkers, Tumor - immunology Carcinoma, Renal Cell - genetics Carcinoma, Renal Cell - immunology Carcinoma, Renal Cell - pathology ccRCC chromosomal translocation CPTAC Disease-Free Survival drug targets Exome - genetics Exome Sequencing Female Gene Expression Regulation, Neoplastic - genetics genetic instability Genome, Human - genetics genomics Humans immune infiltration Male metabolism Middle Aged Neoplasm Proteins - genetics Neoplasm Proteins - immunology Oxidative Phosphorylation phosphoproteomics Phosphorylation - genetics Proteogenomics proteomics renal carcinoma renal cell carcinoma Signal Transduction - genetics Transcriptome - genetics Transcriptome - immunology transcriptomics translation (genetics) tumor microenvironment Tumor Microenvironment - genetics Tumor Microenvironment - immunology |
| Title | Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma |
| URI | https://dx.doi.org/10.1016/j.cell.2019.10.007 https://www.ncbi.nlm.nih.gov/pubmed/31675502 https://www.proquest.com/docview/2311656834 https://www.proquest.com/docview/2374194417 https://pubmed.ncbi.nlm.nih.gov/PMC7331093 |
| Volume | 179 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LS8QwEA7LguBFfFsfSwVvUrdtmj6OWlzWJyIu7C0kbYIV7S66e_DfO9O0xVXcg7c-JiWdZCaTdr5vCDnJfB0rL3MdSfE3I6a5Ciakg__I3DCXSkjEO9_dh8NRcD1m4w5JGywMplXWvt_49Mpb11f6tTb706JAjG_ixyGsiAmFoIEiohxRpQjiG1-03jhmzFQxSMDyQboGzpgcL_w4juldyVmV4RX9tTj9Dj5_5lB-W5QG62Stjibtc9PhDdJR5SZZMfUlP7fI7VVDBpHbD0jIMEFK1rcis9OWp9nAMO2JtlOsIGGn0Fn7UeFjq8MUiw1BI7FNRoPLp3To1OUTnAxihJmjdeIyHbBMunmY6AxsVcoo0D4TOqBSU-0qpnUkAg9NMXaFFjqX-EkI9jDSozukW05KtUdsSXUU53kMu7coUF6e-B7IZwhUjYSWyiJeozee1dziWOLilTdJZC8cdc1R13gNdG2R07bN1DBrLJVmzXDwhfnBwfUvbXfcjB0Hw8HbolST-QeHwBaZh2IaLJPB6YVV2iyya8a77StSCMD2zrdItDATWgEk7l68UxbPFYE31sl0E7r_z3c6IKt4ZlbQQ9Kdvc_VEYRGM9mDTcHVTa-ygC9hxQ4B |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LT8MwDLZ4CMEF8WY8i8QNFdqmWdsjVKANBkIIpN2ipE3EEHQIxoF_j920FQOxA7eqcarUsR0nsT8DHGaBibWfea5idM1IYa6SS-XSHZnXzpWWivKdr2_anYfwss_7U5DWuTAUVlnZfmvTS2tdvTmpuHnyOhhQjm8SxG1cEROGTgOLpmEWvQGPRLvbP2vMccy5LWOQoOojeZU5Y4O86HSc4ruS4zLEK_prdfrtff4Movy2Kl0swWLlTjqndsTLMKWLFZizBSY_V6HXrdEgcueWEBmGhMn6MsictAFqtnmYztA4KZWQcFIcrHOn6bPlY0rVhrCTXIOHi_P7tONW9RPcDJ2EkWtM4nET8kx5eTsxGSqrUlFoAi5NyJRhxtPcmEiGPuli7EkjTa7oTAg3Mcpn6zBTDAu9CY5iJorzPMbtWxRqP08CH-kzylSNpFG6BX7NN5FV4OJU4-JZ1FFkT4J4LYjX9A553YKjps-rhdaYSM3r6RBjAiLQ9k_sd1DPnUDNoWZZ6OHHu0DPlqCHYhZOoiH5ojJtLdiw892MlTAEcH8XtCAak4SGgJC7x1uKwWOJ4E2FMr2Ebf3zn_ZhvnN_3RO97s3VNixQi11Od2Bm9Pahd9FPGqm9Ug--AKD8ECs |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Integrated+Proteogenomic+Characterization+of+Clear+Cell+Renal+Cell+Carcinoma&rft.jtitle=Cell&rft.au=Clark%2C+David+J.&rft.au=Dhanasekaran%2C+Saravana+M.&rft.au=Petralia%2C+Francesca&rft.au=Pan%2C+Jianbo&rft.date=2019-10-31&rft.issn=0092-8674&rft.eissn=1097-4172&rft.volume=179&rft.issue=4&rft.spage=964&rft.epage=983.e31&rft_id=info:doi/10.1016%2Fj.cell.2019.10.007&rft_id=info%3Apmid%2F31675502&rft.externalDocID=PMC7331093 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0092-8674&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0092-8674&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0092-8674&client=summon |