Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 diffe...
Saved in:
| Published in | Cell Vol. 158; no. 6; pp. 1431 - 1443 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
11.09.2014
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2014.08.009 |
Cover
| Abstract | Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes. |
|---|---|
| AbstractList | Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes. Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ~1% of all eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ~34% of the ~170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in ChIP-seq peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif “library” ( http://cisbp.ccbr.utoronto.ca ) can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes. Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes. |
| Author | Ratsch, Gunnar Hughes, Timothy R. Najafabadi, Hamed S. Weirauch, Matthew T. Albu, Mihai van Bakel, Harm Shaulsky, Gad Walhout, Albertha J.M. Reece-Hoyes, John S. Galli, Mary Drewe, Philipp Montenegro-Montero, Alejandro Govindarajan, Sridhar Huang, Eryong Mann, Ishminder Larrondo, Luis F. Cote, Atina G. Mukherjee, Tuhin Lozano, Jean-Claude Lewsey, Mathew G. Ecker, Joseph R. Lambert, Samuel A. Chen, Xiaoting Bouget, François-Yves Yang, Ally Cook, Kate Zheng, Hong Goity, Alejandra |
| AuthorAffiliation | 14 Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 9 Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 2 Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1 5 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8 4 Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA 10065 8 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 11 Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH, USA 45221 12 Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA 01655 6 Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA 10029 7 Sorbonne Universités, UPMC Univ Paris 06, CNRS |
| AuthorAffiliation_xml | – name: 5 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8 – name: 13 DNA2.0 Inc, Menlo Park, CA, USA 94025 – name: 12 Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA 01655 – name: 6 Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA 10029 – name: 11 Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH, USA 45221 – name: 7 Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, CNRS, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France – name: 10 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA 77030 – name: 3 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile 8331150 – name: 8 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 – name: 9 Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 – name: 1 Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA 45229 – name: 14 Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA 92037 – name: 4 Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA 10065 – name: 2 Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1 |
| Author_xml | – sequence: 1 givenname: Matthew T. surname: Weirauch fullname: Weirauch, Matthew T. – sequence: 2 givenname: Ally surname: Yang fullname: Yang, Ally – sequence: 3 givenname: Mihai surname: Albu fullname: Albu, Mihai – sequence: 4 givenname: Atina G. surname: Cote fullname: Cote, Atina G. – sequence: 5 givenname: Alejandro surname: Montenegro-Montero fullname: Montenegro-Montero, Alejandro – sequence: 6 givenname: Philipp surname: Drewe fullname: Drewe, Philipp – sequence: 7 givenname: Hamed S. surname: Najafabadi fullname: Najafabadi, Hamed S. – sequence: 8 givenname: Samuel A. surname: Lambert fullname: Lambert, Samuel A. – sequence: 9 givenname: Ishminder surname: Mann fullname: Mann, Ishminder – sequence: 10 givenname: Kate surname: Cook fullname: Cook, Kate – sequence: 11 givenname: Hong surname: Zheng fullname: Zheng, Hong – sequence: 12 givenname: Alejandra surname: Goity fullname: Goity, Alejandra – sequence: 13 givenname: Harm surname: van Bakel fullname: van Bakel, Harm – sequence: 14 givenname: Jean-Claude surname: Lozano fullname: Lozano, Jean-Claude – sequence: 15 givenname: Mary surname: Galli fullname: Galli, Mary – sequence: 16 givenname: Mathew G. surname: Lewsey fullname: Lewsey, Mathew G. – sequence: 17 givenname: Eryong surname: Huang fullname: Huang, Eryong – sequence: 18 givenname: Tuhin surname: Mukherjee fullname: Mukherjee, Tuhin – sequence: 19 givenname: Xiaoting surname: Chen fullname: Chen, Xiaoting – sequence: 20 givenname: John S. surname: Reece-Hoyes fullname: Reece-Hoyes, John S. – sequence: 21 givenname: Sridhar surname: Govindarajan fullname: Govindarajan, Sridhar – sequence: 22 givenname: Gad surname: Shaulsky fullname: Shaulsky, Gad – sequence: 23 givenname: Albertha J.M. surname: Walhout fullname: Walhout, Albertha J.M. – sequence: 24 givenname: François-Yves surname: Bouget fullname: Bouget, François-Yves – sequence: 25 givenname: Gunnar surname: Ratsch fullname: Ratsch, Gunnar – sequence: 26 givenname: Luis F. surname: Larrondo fullname: Larrondo, Luis F. – sequence: 27 givenname: Joseph R. surname: Ecker fullname: Ecker, Joseph R. – sequence: 28 givenname: Timothy R. surname: Hughes fullname: Hughes, Timothy R. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25215497$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFkc1O3DAUha0KVAboC3RRZckm4V7HTpwNEuKnRUJiMbC2PI4Nnmbswc4g8fZ1BopaFrCyZX_36Nxz9smOD94Q8h2hQsDmeFlpMwwVBWQViAqg-0JmCF1bMmzpDpnlF1qKpmV7ZD-lJQAIzvlXskc5Rc66dkbm52Y0ceW8Gl3whfJ9ceWticZrUwRbXGx-q_gcRqeL26h80tGtt-Sl0mOIxdw8brbsfG20s0678fmQ7Fo1JPPt9Twgd5cXt2e_yuubn1dnp9el5oBjyahGbZkSqBrRQt8zqtiiN7zmQjWG09qyRd3q1uaLsFxhj01jLQDrKENWH5CTF931ZrEyvTZ-jGqQ6-hW2bMMysn_f7x7kPfhSTJsamCYBY5eBWLIa6RRrlyaMlXehE2SNCdGkSF-jiJvsBNQ88nWj39tvfn5G3oG6AugY0gpGvuGIMipWbmUk7ScmpUgZO4xD4l3QznqbWl5NTd8NPoHvJWrKw |
| CitedBy_id | crossref_primary_10_1186_s13059_020_01996_3 crossref_primary_10_1016_j_cell_2016_03_015 crossref_primary_10_1093_bioinformatics_bty600 crossref_primary_10_1073_pnas_2116505119 crossref_primary_10_1016_j_xplc_2023_100717 crossref_primary_10_3390_ijms20194951 crossref_primary_10_1093_nar_gkab853 crossref_primary_10_1002_fsn3_1375 crossref_primary_10_7554_eLife_59157 crossref_primary_10_1111_tpj_15315 crossref_primary_10_1007_s11103_018_0796_8 crossref_primary_10_1016_j_stem_2020_05_001 crossref_primary_10_1016_j_celrep_2017_03_039 crossref_primary_10_1111_pce_14798 crossref_primary_10_1093_nar_gkx276 crossref_primary_10_1021_acssynbio_3c00078 crossref_primary_10_1038_s41592_021_01077_8 crossref_primary_10_1093_genetics_iyac010 crossref_primary_10_1002_wdev_374 crossref_primary_10_1038_s41593_024_01658_8 crossref_primary_10_7554_eLife_73225 crossref_primary_10_3390_pharmaceutics14071464 crossref_primary_10_1016_j_cpb_2016_12_001 crossref_primary_10_1002_art_42390 crossref_primary_10_3389_fpls_2022_998400 crossref_primary_10_1007_s10482_022_01746_4 crossref_primary_10_1016_j_dib_2017_03_027 crossref_primary_10_7554_eLife_59388 crossref_primary_10_1111_tpj_16899 crossref_primary_10_1038_s41586_019_1318_9 crossref_primary_10_1038_srep33351 crossref_primary_10_1016_j_cpb_2015_09_001 crossref_primary_10_1038_s41586_020_2528_x crossref_primary_10_1093_nar_gkv1035 crossref_primary_10_15252_msb_20199174 crossref_primary_10_1016_j_molp_2021_04_013 crossref_primary_10_1111_acel_13047 crossref_primary_10_1016_j_mce_2019_110631 crossref_primary_10_1038_s41467_023_37213_5 crossref_primary_10_1186_s12920_016_0178_5 crossref_primary_10_1016_j_molimm_2022_12_005 crossref_primary_10_1016_j_gpb_2022_05_007 crossref_primary_10_15252_msb_20167131 crossref_primary_10_1016_j_celrep_2019_06_034 crossref_primary_10_1007_s00299_020_02523_1 crossref_primary_10_1016_j_cell_2021_06_023 crossref_primary_10_1093_bib_bbab273 crossref_primary_10_1038_s41586_020_2940_2 crossref_primary_10_1016_j_csbj_2024_05_019 crossref_primary_10_1038_ncomms9717 crossref_primary_10_1093_bib_bbz082 crossref_primary_10_7554_eLife_63632 crossref_primary_10_1093_nar_gkz672 crossref_primary_10_1111_tpj_14443 crossref_primary_10_1016_j_coisb_2017_04_009 crossref_primary_10_1038_s41467_023_36535_8 crossref_primary_10_1016_j_ygeno_2020_08_028 crossref_primary_10_1016_j_xgen_2022_100098 crossref_primary_10_1093_nar_gkv1249 crossref_primary_10_1016_j_isci_2018_09_003 crossref_primary_10_1016_j_stemcr_2023_10_018 crossref_primary_10_1093_bib_bbaa177 crossref_primary_10_1111_tpj_15547 crossref_primary_10_1016_j_xpro_2022_101382 crossref_primary_10_1371_journal_pcbi_1005638 crossref_primary_10_1016_j_celrep_2017_10_001 crossref_primary_10_1038_s41467_020_15654_6 crossref_primary_10_1093_gbe_evx127 crossref_primary_10_1371_journal_pgen_1005981 crossref_primary_10_1038_s41588_025_02081_w crossref_primary_10_1016_j_cell_2016_03_041 crossref_primary_10_1038_s41467_025_56212_2 crossref_primary_10_1038_s41467_019_12291_6 crossref_primary_10_1016_j_celrep_2022_111247 crossref_primary_10_1105_tpc_19_00716 crossref_primary_10_1101_gr_184671_114 crossref_primary_10_1128_mbio_03030_24 crossref_primary_10_7554_eLife_06821 crossref_primary_10_3389_fpls_2019_01030 crossref_primary_10_1186_s12915_022_01450_9 crossref_primary_10_7554_eLife_49558 crossref_primary_10_1007_s11692_017_9440_9 crossref_primary_10_1016_j_molcel_2025_01_014 crossref_primary_10_1111_cns_14603 crossref_primary_10_3389_fpls_2022_1106123 crossref_primary_10_1093_gbe_evz134 crossref_primary_10_1093_nar_gkac992 crossref_primary_10_1126_sciadv_abd7459 crossref_primary_10_1016_j_semcdb_2016_06_017 crossref_primary_10_3390_plants12071452 crossref_primary_10_1073_pnas_2320240121 crossref_primary_10_1038_s41593_021_00803_x crossref_primary_10_1007_s12038_022_00267_6 crossref_primary_10_1042_EBC20190033 crossref_primary_10_1101_gr_276542_121 crossref_primary_10_3390_ijms241612894 crossref_primary_10_3389_fgene_2021_652189 crossref_primary_10_1186_s13059_023_02885_1 crossref_primary_10_1016_j_immuni_2020_10_010 crossref_primary_10_1038_mi_2015_98 crossref_primary_10_1186_s12864_018_4943_z crossref_primary_10_1093_bioinformatics_btw489 crossref_primary_10_1093_nar_gkab877 crossref_primary_10_1038_s41467_020_14974_x crossref_primary_10_1093_plcell_koac079 crossref_primary_10_1371_journal_pone_0294724 crossref_primary_10_1016_j_ccell_2019_10_005 crossref_primary_10_1038_s41590_019_0565_0 crossref_primary_10_1038_s41586_020_2023_4 crossref_primary_10_1007_s10815_023_02947_0 crossref_primary_10_3389_fpls_2022_970018 crossref_primary_10_1136_annrheumdis_2019_215567 crossref_primary_10_1371_journal_pgen_1006401 crossref_primary_10_1186_s13068_017_0807_z crossref_primary_10_7554_eLife_77408 crossref_primary_10_1089_cbr_2020_4314 crossref_primary_10_1186_s12864_023_09692_9 crossref_primary_10_4137_CIN_S39366 crossref_primary_10_1101_gr_279621_124 crossref_primary_10_1016_j_stem_2019_09_010 crossref_primary_10_1038_s41467_020_15512_5 crossref_primary_10_12688_f1000research_17976_1 crossref_primary_10_12688_f1000research_17976_2 crossref_primary_10_1002_pmic_202000034 crossref_primary_10_1128_aem_00360_23 crossref_primary_10_1093_genetics_iyaa044 crossref_primary_10_3389_fpls_2022_938545 crossref_primary_10_3390_biology11010071 crossref_primary_10_1093_bioinformatics_btx563 crossref_primary_10_1038_nrg_2017_8 crossref_primary_10_1038_s41598_024_64324_w crossref_primary_10_1016_j_compbiomed_2022_105993 crossref_primary_10_1101_gr_226233_117 crossref_primary_10_1016_j_cmet_2021_01_001 crossref_primary_10_1038_s41467_023_42445_6 crossref_primary_10_1016_j_celrep_2014_11_038 crossref_primary_10_1016_j_celrep_2023_112665 crossref_primary_10_1016_j_xplc_2023_100558 crossref_primary_10_1093_bioinformatics_btx115 crossref_primary_10_1093_jxb_erw347 crossref_primary_10_7554_eLife_64906 crossref_primary_10_1016_j_ympev_2018_06_043 crossref_primary_10_1073_pnas_2210300120 crossref_primary_10_1038_s41586_024_07348_6 crossref_primary_10_1093_bioinformatics_btaa476 crossref_primary_10_7554_eLife_64903 crossref_primary_10_1021_acs_jpcb_6b12450 crossref_primary_10_7554_eLife_13550 crossref_primary_10_1016_j_stem_2020_07_003 crossref_primary_10_1021_acs_jafc_3c05638 crossref_primary_10_1038_s41421_021_00342_6 crossref_primary_10_1038_s41438_021_00529_8 crossref_primary_10_1016_j_gene_2017_10_079 crossref_primary_10_1038_s41598_018_34506_4 crossref_primary_10_1093_nar_gkx1279 crossref_primary_10_1371_journal_pone_0184500 crossref_primary_10_1038_s41467_018_03256_2 crossref_primary_10_1158_1541_7786_MCR_17_0185 crossref_primary_10_2139_ssrn_3800381 crossref_primary_10_1038_s41467_020_19319_2 crossref_primary_10_1186_s12879_021_05777_6 crossref_primary_10_7554_eLife_04837 crossref_primary_10_1126_science_abg4696 crossref_primary_10_1038_s41592_022_01562_8 crossref_primary_10_1038_s41467_024_49477_6 crossref_primary_10_1093_bioinformatics_btx583 crossref_primary_10_1038_s41588_024_01678_x crossref_primary_10_1016_j_celrep_2025_115240 crossref_primary_10_1038_s41590_021_01086_x crossref_primary_10_1080_15592294_2019_1590085 crossref_primary_10_1371_journal_pone_0233543 crossref_primary_10_1038_s41590_023_01578_y crossref_primary_10_3389_fpls_2017_01341 crossref_primary_10_1038_s41587_022_01551_4 crossref_primary_10_1093_nar_gkaa384 crossref_primary_10_3390_jdb11030032 crossref_primary_10_1093_nar_gkae743 crossref_primary_10_1104_pp_114_248716 crossref_primary_10_1016_j_molcel_2022_06_029 crossref_primary_10_1016_j_xpro_2024_103501 crossref_primary_10_1371_journal_pcbi_1008296 crossref_primary_10_1101_gr_276606_122 crossref_primary_10_1101_gr_277950_123 crossref_primary_10_1016_j_cub_2022_02_040 crossref_primary_10_1038_s41588_021_00947_3 crossref_primary_10_1093_nar_gkae706 crossref_primary_10_1093_nar_gkad615 crossref_primary_10_1093_nar_gkv919 crossref_primary_10_1186_s12864_020_07291_6 crossref_primary_10_1093_nar_gkab676 crossref_primary_10_1093_nar_gkad853 crossref_primary_10_1016_j_bpj_2021_04_002 crossref_primary_10_1186_s12915_017_0469_0 crossref_primary_10_1016_j_celrep_2021_109952 crossref_primary_10_1093_bioinformatics_btaa492 crossref_primary_10_1093_nargab_lqae123 crossref_primary_10_1093_plcell_koae050 crossref_primary_10_1093_nar_gkx1252 crossref_primary_10_1371_journal_pgen_1009039 crossref_primary_10_3390_life14040470 crossref_primary_10_1016_j_ijbiomac_2025_141058 crossref_primary_10_1093_nar_gkz273 crossref_primary_10_12688_f1000research_75471_2 crossref_primary_10_12688_f1000research_75471_1 crossref_primary_10_1093_nar_gkae950 crossref_primary_10_1016_j_immuni_2019_06_001 crossref_primary_10_1016_j_plantsci_2018_06_021 crossref_primary_10_1371_journal_pgen_1010021 crossref_primary_10_1186_s13072_015_0012_x crossref_primary_10_12688_f1000research_75471_3 crossref_primary_10_1038_s41594_020_0488_3 crossref_primary_10_3390_agronomy14081679 crossref_primary_10_1007_s00018_018_2748_5 crossref_primary_10_1093_nar_gkae718 crossref_primary_10_1128_mbio_03291_22 crossref_primary_10_1126_science_aad2257 crossref_primary_10_1007_s00497_021_00432_1 crossref_primary_10_1371_journal_pbio_3002354 crossref_primary_10_1007_s12185_024_03806_z crossref_primary_10_1038_s41467_024_50710_5 crossref_primary_10_1093_bib_bbaa326 crossref_primary_10_1101_gr_200535_115 crossref_primary_10_1038_s41598_024_53578_z crossref_primary_10_1186_s12864_016_2916_7 crossref_primary_10_1126_science_aax8862 crossref_primary_10_1016_j_celrep_2025_115267 crossref_primary_10_2503_hortj_QH_R002 crossref_primary_10_1186_s13227_018_0111_4 crossref_primary_10_1093_nar_gkw1036 crossref_primary_10_1101_gr_275145_120 crossref_primary_10_1109_ACCESS_2019_2961260 crossref_primary_10_1038_s41467_023_40505_5 crossref_primary_10_1080_15592294_2018_1469894 crossref_primary_10_1093_nar_gkz1087 crossref_primary_10_3390_pharmaceutics15030765 crossref_primary_10_1161_CIRCRESAHA_118_314460 crossref_primary_10_1186_s12864_023_09498_9 crossref_primary_10_1016_j_ncrops_2024_100059 crossref_primary_10_1093_bioinformatics_btac696 crossref_primary_10_1098_rspb_2019_0470 crossref_primary_10_1038_s41540_021_00208_3 crossref_primary_10_1093_nar_gkv1463 crossref_primary_10_1007_s10048_018_0546_8 crossref_primary_10_1002_imt2_70009 crossref_primary_10_1073_pnas_1804663115 crossref_primary_10_1093_genetics_iyac056 crossref_primary_10_1016_j_celrep_2023_112220 crossref_primary_10_1002_biot_202100239 crossref_primary_10_26508_lsa_202402719 crossref_primary_10_1186_s12859_018_2242_y crossref_primary_10_1515_jib_2021_0038 crossref_primary_10_1093_nar_gky1297 crossref_primary_10_7554_eLife_25751 crossref_primary_10_1093_nar_gkae535 crossref_primary_10_1093_nar_gky1057 crossref_primary_10_1056_NEJMoa1612665 crossref_primary_10_1042_ETLS20160025 crossref_primary_10_1093_bioinformatics_btx381 crossref_primary_10_1186_s13293_024_00659_3 crossref_primary_10_1038_s41576_018_0069_z crossref_primary_10_15252_msb_202110473 crossref_primary_10_3389_fpls_2020_00075 crossref_primary_10_1073_pnas_1611228113 crossref_primary_10_7554_eLife_09492 crossref_primary_10_1038_s41598_022_21732_0 crossref_primary_10_7554_eLife_66034 crossref_primary_10_1002_0471250953_bi0215s51 crossref_primary_10_1007_s12035_018_0995_y crossref_primary_10_1111_gcbb_12862 crossref_primary_10_1038_srep41174 crossref_primary_10_1016_j_ijbiomac_2024_137729 crossref_primary_10_3389_fgene_2018_00016 crossref_primary_10_7554_eLife_64090 crossref_primary_10_1016_j_celrep_2023_112210 crossref_primary_10_1093_nar_gkad693 crossref_primary_10_1016_j_celrep_2023_112212 crossref_primary_10_1038_s41467_023_38096_2 crossref_primary_10_1038_s41598_017_14167_5 crossref_primary_10_1093_nargab_lqab052 crossref_primary_10_1186_s12915_023_01665_4 crossref_primary_10_1038_s41467_024_47396_0 crossref_primary_10_1038_s41588_024_01806_7 crossref_primary_10_1016_j_devcel_2023_07_007 crossref_primary_10_1186_s12915_021_01078_1 crossref_primary_10_1371_journal_pcbi_1010116 crossref_primary_10_3390_ijms20164005 crossref_primary_10_1128_mBio_01452_15 crossref_primary_10_1007_s10725_020_00620_5 crossref_primary_10_1016_j_pbi_2023_102454 crossref_primary_10_1002_1873_3468_13757 crossref_primary_10_1007_s00299_017_2130_3 crossref_primary_10_3390_ijms21249517 crossref_primary_10_7554_eLife_49921 crossref_primary_10_7554_eLife_56450 crossref_primary_10_1038_s41467_022_30770_1 crossref_primary_10_1016_j_pld_2024_03_008 crossref_primary_10_7554_eLife_46418 crossref_primary_10_1038_s41598_022_20682_x crossref_primary_10_1038_s41467_023_36897_z crossref_primary_10_1038_s41588_024_01904_6 crossref_primary_10_1016_j_celrep_2023_112671 crossref_primary_10_1093_g3journal_jkad004 crossref_primary_10_1093_nar_gkae521 crossref_primary_10_1016_j_pbi_2020_01_003 crossref_primary_10_1038_s41590_024_02075_6 crossref_primary_10_1186_s13059_022_02807_7 crossref_primary_10_1093_nar_gky1081 crossref_primary_10_1016_j_celrep_2024_114965 crossref_primary_10_1016_j_celrep_2014_08_019 crossref_primary_10_3390_life11101010 crossref_primary_10_1242_dev_127365 crossref_primary_10_31083_j_fbs1601004 crossref_primary_10_1371_journal_ppat_1007734 crossref_primary_10_1016_j_cels_2023_06_010 crossref_primary_10_1038_s41556_024_01435_6 crossref_primary_10_1111_cas_13702 crossref_primary_10_1126_science_aav1898 crossref_primary_10_1038_s41467_019_11957_5 crossref_primary_10_1093_nar_gkw982 crossref_primary_10_1126_science_aad7993 crossref_primary_10_1038_s41586_022_04739_5 crossref_primary_10_1038_s41588_018_0278_6 crossref_primary_10_3389_fbioe_2024_1350722 crossref_primary_10_1016_j_celrep_2023_113351 crossref_primary_10_1093_gbe_evae241 crossref_primary_10_1038_s41586_022_05309_5 crossref_primary_10_1093_nar_gkac393 crossref_primary_10_3390_genes10110865 crossref_primary_10_1016_j_gde_2019_07_010 crossref_primary_10_1186_s13059_017_1287_y crossref_primary_10_1101_gr_279037_124 crossref_primary_10_1186_s12881_018_0708_4 crossref_primary_10_1038_s41586_022_05636_7 crossref_primary_10_1534_genetics_118_301116 crossref_primary_10_1093_nargab_lqae178 crossref_primary_10_1016_j_isci_2023_108747 crossref_primary_10_26508_lsa_202201870 crossref_primary_10_3390_plants13071007 crossref_primary_10_1038_s41467_022_35041_7 crossref_primary_10_1186_s12915_020_00862_9 crossref_primary_10_1093_nar_gkab1113 crossref_primary_10_1242_dev_200984 crossref_primary_10_1016_j_tig_2021_04_008 crossref_primary_10_3389_fmolb_2020_614427 crossref_primary_10_1371_journal_pcbi_1010524 crossref_primary_10_1126_science_abn5800 crossref_primary_10_1126_science_aau0730 crossref_primary_10_3389_fgene_2020_565836 crossref_primary_10_1007_s10955_018_1975_3 crossref_primary_10_1016_j_ydbio_2017_03_020 crossref_primary_10_1002_wrna_1508 crossref_primary_10_1016_j_foodres_2024_114939 crossref_primary_10_1038_s41598_017_07761_0 crossref_primary_10_1016_j_cels_2019_05_012 crossref_primary_10_1080_15592294_2024_2309826 crossref_primary_10_1186_s13059_020_02110_3 crossref_primary_10_1016_j_cell_2016_07_012 crossref_primary_10_1111_nph_14734 crossref_primary_10_1038_s41467_019_12624_5 crossref_primary_10_7554_eLife_83979 crossref_primary_10_1038_s42003_022_03531_5 crossref_primary_10_1007_s42994_023_00121_9 crossref_primary_10_1186_s12284_017_0164_3 crossref_primary_10_1016_j_tig_2014_12_003 crossref_primary_10_3390_ijms252413588 crossref_primary_10_7554_eLife_19272 crossref_primary_10_1093_insilicoplants_diz008 crossref_primary_10_1038_nmeth_3156 crossref_primary_10_1038_s41467_022_35076_w crossref_primary_10_1109_JPROC_2015_2494198 crossref_primary_10_1161_CIRCRESAHA_124_324455 crossref_primary_10_1093_bioinformatics_btae110 crossref_primary_10_1371_journal_pgen_1009309 crossref_primary_10_1016_j_plantsci_2017_06_011 crossref_primary_10_2217_pgs_2015_0013 crossref_primary_10_1038_s41598_020_76139_6 crossref_primary_10_1038_s43018_024_00863_5 crossref_primary_10_1093_molbev_msw165 crossref_primary_10_1371_journal_pone_0263322 crossref_primary_10_1186_s12859_018_2486_6 crossref_primary_10_1371_journal_pcbi_1007329 crossref_primary_10_1093_bioinformatics_btad267 crossref_primary_10_1534_g3_117_300296 crossref_primary_10_1038_s44320_024_00038_5 crossref_primary_10_1093_nargab_lqae149 crossref_primary_10_1371_journal_pone_0161659 crossref_primary_10_1038_s41467_019_11955_7 crossref_primary_10_1016_j_ydbio_2017_02_005 crossref_primary_10_1093_bioinformatics_btad271 crossref_primary_10_1074_jbc_RA119_009779 crossref_primary_10_1016_j_cell_2018_05_061 crossref_primary_10_1038_ng_3467 crossref_primary_10_3390_ijms23168981 crossref_primary_10_1038_s41467_024_55440_2 crossref_primary_10_1101_gr_234633_118 crossref_primary_10_1007_s00425_015_2453_7 crossref_primary_10_1093_toxsci_kfv084 crossref_primary_10_3389_fgene_2015_00322 crossref_primary_10_1038_s41598_022_24550_6 crossref_primary_10_1093_nar_gkw313 crossref_primary_10_3389_fpls_2019_00626 crossref_primary_10_1093_molbev_msv058 crossref_primary_10_15252_embr_202051813 crossref_primary_10_1038_s41598_020_77648_0 crossref_primary_10_1186_s13059_021_02503_y crossref_primary_10_1016_j_neuron_2021_12_034 crossref_primary_10_1093_nar_gkx1106 crossref_primary_10_1038_s41467_021_21534_4 crossref_primary_10_1093_gigascience_giae109 crossref_primary_10_1186_s12964_015_0123_9 crossref_primary_10_1186_s12859_018_2255_6 crossref_primary_10_3390_ijms22083813 crossref_primary_10_1007_s00299_019_02433_x crossref_primary_10_1093_narcan_zcad037 crossref_primary_10_1371_journal_pone_0230218 crossref_primary_10_1111_mmi_14843 crossref_primary_10_1016_j_cell_2025_02_017 crossref_primary_10_3390_genes14081638 crossref_primary_10_1186_s12864_017_3566_0 crossref_primary_10_15252_msb_202110625 crossref_primary_10_1111_nph_13687 crossref_primary_10_3389_fcell_2024_1356589 crossref_primary_10_1016_j_molcel_2019_10_004 crossref_primary_10_1172_JCI170848 crossref_primary_10_1186_s13059_017_1189_z crossref_primary_10_1016_j_celrep_2021_108891 crossref_primary_10_1111_tpj_15189 crossref_primary_10_1093_nar_gky1112 crossref_primary_10_1371_journal_pntd_0008275 crossref_primary_10_1584_jpestics_W22_24 crossref_primary_10_3390_ijms23137262 crossref_primary_10_1126_scitranslmed_abg4328 crossref_primary_10_1186_s13059_019_1750_z crossref_primary_10_1038_s41467_022_33781_0 crossref_primary_10_7554_eLife_90136_3 crossref_primary_10_1038_s41590_019_0471_5 crossref_primary_10_1038_s41477_021_00894_1 crossref_primary_10_3389_fpls_2021_660303 crossref_primary_10_7554_eLife_50065 crossref_primary_10_1038_s41588_020_00738_2 crossref_primary_10_1111_tpj_16483 crossref_primary_10_1073_pnas_1817621116 crossref_primary_10_7554_eLife_82459 crossref_primary_10_1016_j_cell_2018_05_029 crossref_primary_10_1016_j_ydbio_2018_11_006 crossref_primary_10_1093_nar_gkaa1155 crossref_primary_10_1007_s00299_015_1904_8 crossref_primary_10_1111_mpp_12844 crossref_primary_10_1093_bib_bbad156 crossref_primary_10_1158_2159_8290_CD_19_1500 crossref_primary_10_1016_j_csbj_2021_05_039 crossref_primary_10_1016_j_molp_2015_08_008 crossref_primary_10_1016_j_cell_2018_05_019 crossref_primary_10_1093_bib_bbad147 crossref_primary_10_3390_genes11090995 crossref_primary_10_1038_s41586_022_05279_8 crossref_primary_10_1002_ece3_10571 crossref_primary_10_1021_acsomega_0c04069 crossref_primary_10_1093_nar_gkaf031 crossref_primary_10_1101_gr_270751_120 crossref_primary_10_1016_j_celrep_2023_113180 crossref_primary_10_1016_j_ibmb_2020_103333 crossref_primary_10_3389_fpls_2023_1212073 crossref_primary_10_1016_j_molcel_2024_06_022 crossref_primary_10_1093_bioadv_vbad055 crossref_primary_10_1038_nbt_3343 crossref_primary_10_1016_j_cels_2018_12_001 crossref_primary_10_1016_j_devcel_2018_11_009 crossref_primary_10_1093_nar_gkaa1137 crossref_primary_10_1111_tpj_14281 crossref_primary_10_12688_f1000research_7408_1 crossref_primary_10_1016_j_omtn_2024_102234 crossref_primary_10_1093_nar_gkaa1134 crossref_primary_10_1016_j_immuni_2019_03_031 crossref_primary_10_1038_s41559_017_0447_5 crossref_primary_10_3389_fgene_2021_667866 crossref_primary_10_1038_s41467_022_33785_w crossref_primary_10_1038_s41587_023_01747_2 crossref_primary_10_12688_f1000research_7408_2 crossref_primary_10_1038_s41419_023_06373_z crossref_primary_10_1146_annurev_cellbio_111315_124922 crossref_primary_10_1371_journal_pgen_1009955 crossref_primary_10_1016_j_gpb_2019_11_015 crossref_primary_10_1186_s12885_021_09048_0 crossref_primary_10_1016_j_heliyon_2024_e38500 crossref_primary_10_7554_eLife_51139 crossref_primary_10_1016_j_ydbio_2018_11_013 crossref_primary_10_1016_j_jmb_2023_168121 crossref_primary_10_1038_ng_3682 crossref_primary_10_3390_plants9020166 crossref_primary_10_1128_spectrum_03651_22 crossref_primary_10_1093_molbev_msab007 crossref_primary_10_3389_fcell_2020_569601 crossref_primary_10_3389_fpls_2022_870078 crossref_primary_10_1007_s43032_019_00075_8 crossref_primary_10_1038_s12276_022_00769_1 crossref_primary_10_1038_srep21849 crossref_primary_10_1016_j_ydbio_2017_05_005 crossref_primary_10_1016_j_cell_2018_06_031 crossref_primary_10_1016_j_isci_2022_104231 crossref_primary_10_1016_j_xgen_2023_100420 crossref_primary_10_1038_s41467_019_10912_8 crossref_primary_10_1172_jci_insight_179392 crossref_primary_10_26508_lsa_202301988 crossref_primary_10_1038_nbt_3128 crossref_primary_10_1126_science_adj8172 crossref_primary_10_7554_eLife_71358 crossref_primary_10_1371_journal_pone_0169796 crossref_primary_10_1016_j_celrep_2018_11_056 crossref_primary_10_1371_journal_pone_0263307 crossref_primary_10_1016_j_pbi_2015_06_010 crossref_primary_10_1038_s41586_020_1997_2 crossref_primary_10_1093_plcell_koab287 crossref_primary_10_1016_j_celrep_2023_112902 crossref_primary_10_1016_j_cels_2016_09_004 crossref_primary_10_1093_gbe_evz099 crossref_primary_10_1038_s41586_024_08443_4 crossref_primary_10_1021_acsomega_9b00540 crossref_primary_10_1093_plcell_koab281 crossref_primary_10_1186_s13059_022_02713_y crossref_primary_10_3389_fmicb_2023_1129103 crossref_primary_10_1242_dev_202276 crossref_primary_10_1021_jacs_0c05669 crossref_primary_10_1038_s41588_023_01572_y crossref_primary_10_1038_s41467_017_02798_1 crossref_primary_10_1515_med_2021_0264 crossref_primary_10_1016_j_celrep_2024_114367 crossref_primary_10_1016_j_tranon_2024_102192 crossref_primary_10_1038_ng_3861 crossref_primary_10_1038_s41596_024_01026_7 crossref_primary_10_1186_s12864_018_5408_0 crossref_primary_10_1587_nolta_13_415 crossref_primary_10_7554_eLife_70283 crossref_primary_10_1093_bioinformatics_btaa845 crossref_primary_10_1261_rna_080026_124 crossref_primary_10_1038_s41477_022_01289_6 crossref_primary_10_1038_s41467_024_53158_9 crossref_primary_10_1111_tpj_15124 crossref_primary_10_1093_nar_gkaa618 crossref_primary_10_1016_j_ymthe_2021_01_033 crossref_primary_10_1038_s41598_019_50485_6 crossref_primary_10_1126_sciadv_abh1022 crossref_primary_10_1038_s41588_019_0411_1 crossref_primary_10_1016_j_ijbiomac_2025_140630 crossref_primary_10_1038_s41467_024_47280_x crossref_primary_10_1111_evo_13487 crossref_primary_10_1126_science_aat8464 crossref_primary_10_1016_j_gene_2022_146468 crossref_primary_10_1016_j_devcel_2016_09_031 crossref_primary_10_1016_j_gene_2021_146131 crossref_primary_10_1093_plcell_koab267 crossref_primary_10_1172_jci_insight_158895 crossref_primary_10_1093_jxb_erad248 crossref_primary_10_1016_j_celrep_2017_05_069 crossref_primary_10_1007_s00520_017_3883_5 crossref_primary_10_1371_journal_pgen_1010988 crossref_primary_10_1016_j_cell_2016_04_038 crossref_primary_10_1186_s12859_018_2104_7 crossref_primary_10_1093_nar_gky787 crossref_primary_10_1038_ncomms10148 crossref_primary_10_1016_j_pbi_2015_07_001 crossref_primary_10_1093_insilicoplants_diac014 crossref_primary_10_1021_acssynbio_8b00236 crossref_primary_10_1038_ng_3646 crossref_primary_10_1016_j_pbi_2015_07_007 crossref_primary_10_1126_sciadv_adk2082 crossref_primary_10_1093_bib_bbae451 crossref_primary_10_7554_eLife_29656 crossref_primary_10_1016_j_tplants_2018_03_014 crossref_primary_10_1111_jpi_12905 crossref_primary_10_1111_tpj_15586 crossref_primary_10_1111_nph_18720 crossref_primary_10_1007_s12195_024_00812_3 crossref_primary_10_1073_pnas_1719138115 crossref_primary_10_1002_pld3_49 crossref_primary_10_1126_sciadv_aav3262 crossref_primary_10_1126_science_add1250 crossref_primary_10_1016_j_celrep_2022_110877 crossref_primary_10_1016_j_ejbt_2018_08_005 crossref_primary_10_1093_bioadv_vbad031 crossref_primary_10_7554_eLife_51325 crossref_primary_10_1038_srep25164 crossref_primary_10_1158_2159_8290_CD_17_0368 crossref_primary_10_1016_j_xgen_2023_100272 crossref_primary_10_1016_j_csbj_2023_03_032 crossref_primary_10_1093_hmg_ddad177 crossref_primary_10_1093_database_baae109 crossref_primary_10_1371_journal_pbio_2006337 crossref_primary_10_3390_ijms26010386 crossref_primary_10_1016_j_immuni_2021_03_020 crossref_primary_10_1126_sciadv_aao1799 crossref_primary_10_1146_annurev_arplant_043014_115619 crossref_primary_10_3389_fimmu_2024_1428773 crossref_primary_10_1126_science_abg7216 crossref_primary_10_1186_s13059_019_1768_2 crossref_primary_10_1093_hmg_ddad182 crossref_primary_10_1007_s00294_017_0772_x crossref_primary_10_1016_j_cmet_2016_04_002 crossref_primary_10_1158_0008_5472_CAN_18_0454 crossref_primary_10_7554_eLife_77951 crossref_primary_10_1007_s13258_023_01471_w crossref_primary_10_1093_plcell_koab093 crossref_primary_10_1111_tpj_16538 crossref_primary_10_1093_nargab_lqab100 crossref_primary_10_1186_s12864_017_3934_9 crossref_primary_10_1038_s41586_022_05202_1 crossref_primary_10_1111_nph_16248 crossref_primary_10_1016_j_stem_2024_05_008 crossref_primary_10_1111_tpj_13261 crossref_primary_10_1038_s41598_019_50389_5 crossref_primary_10_1093_nargab_lqaa049 crossref_primary_10_3389_fmolb_2022_920492 crossref_primary_10_1093_nar_gkab956 crossref_primary_10_1371_journal_pgen_1011081 crossref_primary_10_3389_fpls_2015_00911 crossref_primary_10_1093_g3journal_jkac009 crossref_primary_10_3390_genes13010073 crossref_primary_10_1073_pnas_2107879119 crossref_primary_10_1016_j_csbj_2020_05_018 crossref_primary_10_1038_s42003_024_06400_5 crossref_primary_10_1038_s41592_019_0367_1 crossref_primary_10_1093_hmg_ddy140 crossref_primary_10_1534_genetics_117_300657 crossref_primary_10_1093_nargab_lqaa046 crossref_primary_10_1186_s12870_016_0932_z crossref_primary_10_1002_pld3_16 crossref_primary_10_1038_s41467_024_55403_7 crossref_primary_10_1038_s41467_022_28067_4 crossref_primary_10_1016_j_cell_2023_02_018 crossref_primary_10_2139_ssrn_4076343 crossref_primary_10_1093_nar_gkx376 crossref_primary_10_1007_s00299_020_02611_2 crossref_primary_10_1093_bib_bbab149 crossref_primary_10_7554_eLife_89702 crossref_primary_10_1093_nar_gkv195 crossref_primary_10_1038_s41467_018_03133_y crossref_primary_10_1093_genetics_iyad004 crossref_primary_10_1371_journal_pgen_1005639 crossref_primary_10_1016_j_pbi_2015_12_011 crossref_primary_10_1016_j_stem_2016_11_006 crossref_primary_10_1093_plphys_kiaa091 crossref_primary_10_1093_bioinformatics_btv466 crossref_primary_10_1534_genetics_114_171124 crossref_primary_10_1007_s11240_024_02838_x crossref_primary_10_1093_bioinformatics_btaa789 crossref_primary_10_1016_j_xgen_2023_100262 crossref_primary_10_1038_s43586_020_00008_9 crossref_primary_10_1183_13993003_00474_2022 crossref_primary_10_1093_hmg_ddz226 crossref_primary_10_1186_s13059_022_02723_w crossref_primary_10_1126_science_abm7993 crossref_primary_10_1371_journal_pcbi_1004429 crossref_primary_10_1093_nar_gkac819 crossref_primary_10_1016_j_cpb_2015_10_001 crossref_primary_10_1016_j_devcel_2022_04_013 crossref_primary_10_1093_nar_gkv1134 crossref_primary_10_1038_s41587_023_01716_9 crossref_primary_10_7554_eLife_69288 crossref_primary_10_1007_s42976_020_00097_y crossref_primary_10_1371_journal_pone_0141044 crossref_primary_10_3389_fpls_2022_942710 crossref_primary_10_1038_s41467_023_38637_9 crossref_primary_10_1093_bioinformatics_btz617 crossref_primary_10_1186_s12864_017_4111_x crossref_primary_10_1093_nar_gkaa687 crossref_primary_10_1111_tpj_15873 crossref_primary_10_1101_gr_277722_123 crossref_primary_10_2139_ssrn_3245213 crossref_primary_10_1002_anie_201905235 crossref_primary_10_1016_j_tplants_2016_01_014 crossref_primary_10_1038_s41586_023_06984_8 crossref_primary_10_1128_mBio_01493_21 crossref_primary_10_1242_dev_200375 crossref_primary_10_1016_j_stem_2019_11_011 crossref_primary_10_1109_TCBB_2020_3024222 crossref_primary_10_1038_srep38715 crossref_primary_10_1016_j_celrep_2018_04_054 crossref_primary_10_1093_bioinformatics_btw338 crossref_primary_10_1158_2159_8290_CD_22_0692 crossref_primary_10_1007_s11427_023_2362_5 crossref_primary_10_1038_s41467_019_10267_0 crossref_primary_10_1371_journal_pone_0290035 crossref_primary_10_1186_s13059_020_02139_4 crossref_primary_10_1038_s41467_021_21854_5 crossref_primary_10_1038_s41467_023_43044_1 crossref_primary_10_2139_ssrn_4156163 crossref_primary_10_3390_metabo13060740 crossref_primary_10_1126_science_aax1971 crossref_primary_10_1038_s41564_018_0289_1 crossref_primary_10_1093_nar_gkac881 crossref_primary_10_7554_eLife_51503 crossref_primary_10_1016_j_jbc_2024_107520 crossref_primary_10_7554_eLife_06967 crossref_primary_10_1016_j_bbagrm_2019_194430 crossref_primary_10_1021_acs_biochem_7b00741 crossref_primary_10_1039_C6IB00079G crossref_primary_10_1073_pnas_1813520115 crossref_primary_10_1016_j_stress_2023_100299 crossref_primary_10_1111_mmi_14160 crossref_primary_10_1093_nar_gkac849 crossref_primary_10_1093_nar_gkx177 crossref_primary_10_1093_nar_gkx174 crossref_primary_10_1146_annurev_cellbio_100617_062719 crossref_primary_10_1126_science_ade0004 crossref_primary_10_1016_j_bbagrm_2019_194447 crossref_primary_10_1038_s41467_024_52296_4 crossref_primary_10_1093_nar_gkad945 crossref_primary_10_1038_ncomms14593 crossref_primary_10_1016_j_bbagrm_2019_194443 crossref_primary_10_1093_nar_gkab765 crossref_primary_10_1093_bioinformatics_btaa580 crossref_primary_10_1186_s13293_024_00634_y crossref_primary_10_1016_j_molcel_2021_03_045 crossref_primary_10_1038_s41598_020_74793_4 crossref_primary_10_1093_plcell_koad054 crossref_primary_10_1016_j_ydbio_2018_10_018 crossref_primary_10_1242_bio_058756 crossref_primary_10_1093_nar_gkv1176 crossref_primary_10_1242_dev_202787 crossref_primary_10_1093_nar_gkz363 crossref_primary_10_18699_vjgb_24_90 crossref_primary_10_1101_gr_226852_117 crossref_primary_10_1093_g3journal_jkab100 crossref_primary_10_1016_j_xgen_2022_100164 crossref_primary_10_1016_j_csbj_2020_04_007 crossref_primary_10_1101_gr_232488_117 crossref_primary_10_1039_C6IB00093B crossref_primary_10_1093_nar_gkae846 crossref_primary_10_1186_s13072_019_0291_8 crossref_primary_10_1007_s00709_016_1045_0 crossref_primary_10_1038_s41467_021_24445_6 crossref_primary_10_1016_j_bbagrm_2016_05_001 crossref_primary_10_1038_s41586_020_2536_x crossref_primary_10_1242_dmm_049790 crossref_primary_10_1016_j_funbio_2018_01_004 crossref_primary_10_1093_bib_bbab521 crossref_primary_10_1371_journal_pcbi_1010011 crossref_primary_10_1093_nar_gkaa252 crossref_primary_10_3390_ijms24119349 crossref_primary_10_1038_s41467_023_36116_9 crossref_primary_10_1093_nar_gkab349 crossref_primary_10_1016_j_csbj_2020_06_012 crossref_primary_10_1128_mbio_03111_24 crossref_primary_10_1182_blood_2023020276 crossref_primary_10_1186_s13293_024_00638_8 crossref_primary_10_3390_jof9040424 crossref_primary_10_1016_j_molcel_2021_12_008 crossref_primary_10_3389_fmicb_2019_01624 crossref_primary_10_1016_j_ygeno_2020_03_028 crossref_primary_10_1016_j_ajhg_2021_05_001 crossref_primary_10_3389_fgene_2020_00457 crossref_primary_10_1016_j_cell_2016_09_034 crossref_primary_10_1016_j_tig_2020_12_001 crossref_primary_10_1016_j_isci_2021_103663 crossref_primary_10_1007_s40778_015_0019_z crossref_primary_10_1016_j_xpro_2023_102279 crossref_primary_10_1038_ni_3683 crossref_primary_10_1242_dev_202529 crossref_primary_10_3389_fgene_2018_00571 crossref_primary_10_1038_s41467_020_16571_4 crossref_primary_10_1038_s41467_024_48774_4 crossref_primary_10_1101_gr_264705_120 crossref_primary_10_1038_s41467_021_25935_3 crossref_primary_10_1021_acs_jctc_7b00849 crossref_primary_10_1093_bib_bbab311 crossref_primary_10_1016_j_cels_2017_06_015 crossref_primary_10_1111_nph_17161 crossref_primary_10_1038_s41388_017_0042_x crossref_primary_10_1038_s41467_024_52154_3 crossref_primary_10_1101_gr_238253_118 crossref_primary_10_1038_s41588_022_01197_7 crossref_primary_10_1016_j_cell_2018_01_029 crossref_primary_10_1146_annurev_arplant_043015_112205 crossref_primary_10_1093_nar_gkac652 crossref_primary_10_3390_vaccines8020246 crossref_primary_10_1038_s41477_018_0160_7 crossref_primary_10_1128_MCB_00499_18 crossref_primary_10_1371_journal_pone_0131415 crossref_primary_10_1186_s12864_017_4305_2 crossref_primary_10_1038_s41559_016_0045 crossref_primary_10_1093_nar_gkac658 crossref_primary_10_1105_tpc_20_00080 crossref_primary_10_1159_000494890 crossref_primary_10_3389_fgene_2021_649764 crossref_primary_10_1038_s41588_024_01982_6 crossref_primary_10_15252_msb_20177902 crossref_primary_10_1016_j_bbrc_2018_04_048 crossref_primary_10_3390_biom10020313 crossref_primary_10_1016_j_copbio_2015_02_001 crossref_primary_10_1038_s41467_019_09522_1 crossref_primary_10_1093_database_baz046 crossref_primary_10_1016_j_gde_2017_02_007 crossref_primary_10_1038_nmeth_4401 crossref_primary_10_1242_dev_200561 crossref_primary_10_1038_s41586_024_07169_7 crossref_primary_10_1371_journal_pgen_1011222 crossref_primary_10_1016_j_cell_2018_10_038 crossref_primary_10_1038_s41592_019_0730_2 crossref_primary_10_1093_bib_bbab533 crossref_primary_10_3390_ijms20153681 crossref_primary_10_1111_tpj_13882 crossref_primary_10_1134_S2079086421040071 crossref_primary_10_1084_jem_20150806 crossref_primary_10_26508_lsa_202402808 crossref_primary_10_1038_s41598_024_54355_8 crossref_primary_10_1073_pnas_1815336116 crossref_primary_10_1093_nar_gkx1126 crossref_primary_10_1016_j_cels_2018_01_002 crossref_primary_10_3390_genes14071476 crossref_primary_10_1016_j_bbagrm_2016_08_005 crossref_primary_10_3390_ijms23010066 crossref_primary_10_1093_nar_gkad318 crossref_primary_10_1016_j_ajhg_2023_12_008 crossref_primary_10_1016_j_xplc_2021_100232 crossref_primary_10_1093_nar_gkad798 crossref_primary_10_1016_j_celrep_2020_107795 crossref_primary_10_1186_s12870_017_1210_4 crossref_primary_10_1038_s41467_025_57480_8 crossref_primary_10_3390_microorganisms9020402 crossref_primary_10_1126_sciimmunol_adf8776 crossref_primary_10_1093_nar_gkaa291 crossref_primary_10_1016_j_bbagrm_2023_194906 crossref_primary_10_1111_tpj_14940 crossref_primary_10_1021_jacs_1c03852 crossref_primary_10_1161_HYPERTENSIONAHA_124_22886 crossref_primary_10_1073_pnas_1603229113 crossref_primary_10_1126_sciadv_adn6625 crossref_primary_10_1073_pnas_1811431115 crossref_primary_10_1016_j_cub_2023_02_073 crossref_primary_10_1007_s00439_021_02305_z crossref_primary_10_3390_ijms231911229 crossref_primary_10_1016_j_jtcvs_2024_04_026 crossref_primary_10_1186_s12859_025_06094_4 crossref_primary_10_1073_pnas_1603577113 crossref_primary_10_1073_pnas_2208795119 crossref_primary_10_1016_j_cell_2022_09_010 crossref_primary_10_1534_genetics_118_300904 crossref_primary_10_1016_j_isci_2021_103468 crossref_primary_10_1002_cpmb_121 crossref_primary_10_1101_gr_188680_114 crossref_primary_10_3389_fmicb_2020_588263 crossref_primary_10_1016_j_celrep_2019_03_071 crossref_primary_10_1093_nar_gkad1225 crossref_primary_10_1016_j_xpro_2022_101926 crossref_primary_10_1111_nph_14943 crossref_primary_10_1093_jxb_erw281 crossref_primary_10_1371_journal_pcbi_1011536 crossref_primary_10_1093_nar_gkab598 crossref_primary_10_1053_j_gastro_2020_01_027 crossref_primary_10_1038_nprot_2017_055 crossref_primary_10_1073_pnas_1620749114 crossref_primary_10_1186_s12859_022_04615_z crossref_primary_10_1016_j_bbagrm_2021_194768 crossref_primary_10_1093_bfgp_elw030 crossref_primary_10_1073_pnas_1603217113 crossref_primary_10_3390_cells10020467 crossref_primary_10_1126_science_adk2055 crossref_primary_10_1038_s41598_018_31101_5 crossref_primary_10_1016_j_ajhg_2015_03_002 crossref_primary_10_3109_10409238_2015_1051505 crossref_primary_10_1038_s41557_023_01196_z crossref_primary_10_1371_journal_pgen_1010187 crossref_primary_10_1038_s41467_022_28659_0 crossref_primary_10_1016_j_bbagrm_2021_194765 crossref_primary_10_1038_s42003_023_05420_x crossref_primary_10_1534_g3_117_043331 crossref_primary_10_1093_bioinformatics_btad217 crossref_primary_10_1093_cercor_bhaa142 crossref_primary_10_1186_s12859_016_1298_9 crossref_primary_10_1016_j_crmeth_2022_100218 crossref_primary_10_1016_j_apsb_2024_04_015 crossref_primary_10_1016_j_plantsci_2023_111921 crossref_primary_10_1093_nar_gkad1240 crossref_primary_10_1371_journal_pbio_3002283 crossref_primary_10_1038_s41587_023_01718_7 crossref_primary_10_1088_1478_3975_ab8697 crossref_primary_10_1038_srep45670 crossref_primary_10_1016_j_ccell_2023_10_008 crossref_primary_10_1161_CIRCULATIONAHA_120_051078 crossref_primary_10_1136_jitc_2022_005532 crossref_primary_10_1038_s41588_024_01892_7 crossref_primary_10_1016_j_jbc_2021_100947 crossref_primary_10_1093_nargab_lqae068 crossref_primary_10_1182_blood_2019004684 crossref_primary_10_1016_j_cmet_2021_04_018 crossref_primary_10_1101_gr_277960_123 crossref_primary_10_1038_s41586_024_07501_1 crossref_primary_10_1002_pld3_133 crossref_primary_10_1186_s12864_024_10630_6 crossref_primary_10_1016_j_gene_2022_146556 crossref_primary_10_1093_nar_gkae210 crossref_primary_10_1126_science_abe1505 crossref_primary_10_3390_genes13061083 crossref_primary_10_1016_j_celrep_2023_113478 crossref_primary_10_1038_s41593_022_01166_7 crossref_primary_10_1073_pnas_2216698120 crossref_primary_10_1128_spectrum_02087_23 crossref_primary_10_1093_nar_gkac1272 crossref_primary_10_1074_jbc_RA117_000485 crossref_primary_10_1007_s11738_024_03701_4 crossref_primary_10_3390_microorganisms11102505 crossref_primary_10_1038_s41467_018_03082_6 crossref_primary_10_1093_jxb_erab190 crossref_primary_10_1186_s13059_023_02955_4 crossref_primary_10_1534_g3_119_400319 crossref_primary_10_1007_s10955_015_1388_5 crossref_primary_10_15252_msb_20177840 crossref_primary_10_3389_fgene_2020_00730 crossref_primary_10_1093_database_baz108 crossref_primary_10_1302_2046_3758_118_BJR_2021_0188_R1 crossref_primary_10_1038_s41592_022_01461_y crossref_primary_10_1093_bioinformatics_btx191 crossref_primary_10_1073_pnas_2009501118 crossref_primary_10_1534_g3_115_020248 crossref_primary_10_1038_nmeth_4143 crossref_primary_10_1101_gr_275472_121 crossref_primary_10_1016_j_csbj_2016_06_004 crossref_primary_10_1093_jxb_erx257 crossref_primary_10_1093_nar_gkx936 crossref_primary_10_1038_s42003_020_01152_4 crossref_primary_10_1016_j_ab_2021_114298 crossref_primary_10_1016_j_cels_2024_08_004 crossref_primary_10_1016_j_chom_2018_03_007 crossref_primary_10_1098_rstb_2016_0416 crossref_primary_10_1126_science_aaj2239 crossref_primary_10_1186_s13059_023_03021_9 crossref_primary_10_1093_bioinformatics_btad373 crossref_primary_10_1093_bioinformatics_btae461 crossref_primary_10_1016_j_molp_2022_10_016 crossref_primary_10_1038_s41594_024_01235_4 crossref_primary_10_1093_nargab_lqae090 crossref_primary_10_1002_wsbm_1411 crossref_primary_10_1101_gr_227231_117 crossref_primary_10_1016_j_molcel_2019_07_009 crossref_primary_10_3389_fevo_2020_564071 crossref_primary_10_1073_pnas_2011795117 crossref_primary_10_1186_s13195_024_01659_6 crossref_primary_10_1002_bies_202300210 crossref_primary_10_1093_bioinformatics_btad378 crossref_primary_10_1021_acs_jpcb_8b04187 crossref_primary_10_7554_eLife_90136 crossref_primary_10_1038_s41467_018_04462_8 crossref_primary_10_1002_pld3_102 crossref_primary_10_1016_j_ydbio_2016_02_031 crossref_primary_10_1021_jacs_2c04824 crossref_primary_10_1038_s41598_017_04936_7 crossref_primary_10_1093_nar_gkae441 crossref_primary_10_1016_j_csbj_2021_11_012 crossref_primary_10_1016_j_molp_2018_10_010 crossref_primary_10_1038_s41588_018_0046_7 crossref_primary_10_3390_genes15050576 crossref_primary_10_1007_s00251_018_1061_7 crossref_primary_10_1093_bioinformatics_btae234 crossref_primary_10_1016_j_celrep_2019_10_033 crossref_primary_10_1016_j_molp_2019_09_002 crossref_primary_10_3390_ijms231911874 crossref_primary_10_3389_fonc_2018_00100 crossref_primary_10_7554_eLife_46726 crossref_primary_10_1038_s41467_021_20950_w crossref_primary_10_1016_j_celrep_2024_114640 crossref_primary_10_1093_nar_gkad1059 crossref_primary_10_1038_s41588_021_01008_5 crossref_primary_10_1002_cpbi_70 crossref_primary_10_1093_nar_gkae012 crossref_primary_10_1186_s12864_016_2549_x crossref_primary_10_1016_j_celrep_2019_12_054 crossref_primary_10_1101_gad_348993_121 crossref_primary_10_1002_advs_202502443 crossref_primary_10_1177_11769343211041382 crossref_primary_10_1016_j_cell_2023_08_042 crossref_primary_10_1016_j_cell_2021_04_024 crossref_primary_10_3389_fnhum_2022_955607 crossref_primary_10_1038_s42003_024_06352_w crossref_primary_10_1038_s41598_019_49741_6 crossref_primary_10_1093_gbe_evv205 crossref_primary_10_1038_s41586_023_06693_2 crossref_primary_10_1186_s12859_018_2343_7 crossref_primary_10_1093_genetics_iyae189 crossref_primary_10_1002_wsbm_1423 crossref_primary_10_1093_nar_gkab1039 crossref_primary_10_1371_journal_pcbi_1006591 crossref_primary_10_1111_nph_15515 crossref_primary_10_1128_AEM_02347_19 crossref_primary_10_1016_j_cmet_2023_09_013 crossref_primary_10_1021_acsomega_3c09670 crossref_primary_10_1093_nar_gkz1020 crossref_primary_10_2217_epi_2020_0424 crossref_primary_10_1126_science_adj0116 crossref_primary_10_1093_nar_gky822 crossref_primary_10_1038_s41467_019_11881_8 crossref_primary_10_1093_nar_gkad1077 crossref_primary_10_1093_gbe_evab273 crossref_primary_10_1007_s42977_021_00089_x crossref_primary_10_1016_j_devcel_2024_02_010 crossref_primary_10_1101_gr_255760_119 crossref_primary_10_1101_gr_260463_119 crossref_primary_10_15252_msb_20209539 crossref_primary_10_1073_pnas_1500605112 crossref_primary_10_1016_j_cels_2018_02_009 crossref_primary_10_1016_j_cell_2023_08_027 crossref_primary_10_1038_s41467_021_22234_9 crossref_primary_10_1038_s41586_023_06936_2 crossref_primary_10_7554_eLife_52370 crossref_primary_10_1016_j_bbagrm_2016_09_003 crossref_primary_10_1002_ange_201905235 crossref_primary_10_1111_nph_19096 crossref_primary_10_1186_s12870_018_1329_y crossref_primary_10_1371_journal_pcbi_1010863 crossref_primary_10_1007_s11427_020_1702_x crossref_primary_10_1016_j_jgg_2023_01_006 crossref_primary_10_1038_s41576_022_00532_2 crossref_primary_10_1371_journal_pgen_1007289 crossref_primary_10_1038_nbt_4138 crossref_primary_10_1016_j_compbiolchem_2019_06_004 crossref_primary_10_7554_eLife_32785 crossref_primary_10_1126_science_aag1550 crossref_primary_10_1016_j_tig_2016_08_009 crossref_primary_10_1038_s41467_020_15022_4 crossref_primary_10_3390_jdb4020016 crossref_primary_10_1093_pcp_pcv156 crossref_primary_10_1007_s00253_019_09733_y crossref_primary_10_1093_plcell_koaa038 crossref_primary_10_1186_s13059_020_1929_3 crossref_primary_10_1186_s12864_022_08486_9 crossref_primary_10_1186_s12864_017_3832_1 crossref_primary_10_1093_nar_gkx314 crossref_primary_10_1152_physiolgenomics_00048_2023 crossref_primary_10_3389_fbinf_2021_777299 crossref_primary_10_3389_fgene_2020_591194 crossref_primary_10_1109_TCBB_2022_3204365 crossref_primary_10_1038_s41592_024_02274_x crossref_primary_10_1021_acschembio_9b00934 crossref_primary_10_1101_gad_310367_117 crossref_primary_10_1016_j_pbi_2021_102136 crossref_primary_10_1038_s41592_023_02086_5 crossref_primary_10_1111_tpj_13097 crossref_primary_10_1101_gr_248823_119 crossref_primary_10_1016_j_cell_2015_03_003 crossref_primary_10_1007_s00253_018_8887_7 crossref_primary_10_1093_bib_bbae110 crossref_primary_10_1109_ACCESS_2020_3042903 crossref_primary_10_1111_tpj_16375 crossref_primary_10_1038_s41467_024_55238_2 crossref_primary_10_1093_biolre_iox028 crossref_primary_10_1016_j_slast_2023_05_001 crossref_primary_10_1038_s41467_018_03921_6 crossref_primary_10_1016_j_immuni_2017_07_012 crossref_primary_10_1158_0008_5472_CAN_21_0730 crossref_primary_10_1038_s41588_022_01149_1 crossref_primary_10_1158_1535_7163_MCT_23_0144 crossref_primary_10_1186_s12864_019_6051_0 crossref_primary_10_3390_cancers12113363 crossref_primary_10_1016_j_ajhg_2019_07_016 crossref_primary_10_1101_gr_222844_117 crossref_primary_10_1038_s41467_020_19829_z crossref_primary_10_1016_j_ydbio_2022_05_019 crossref_primary_10_1101_gr_231886_117 crossref_primary_10_1093_bioinformatics_btaa928 crossref_primary_10_3389_fmicb_2023_1215609 crossref_primary_10_1016_j_cell_2022_11_028 crossref_primary_10_1038_s41591_018_0008_8 crossref_primary_10_1038_s41576_023_00618_5 crossref_primary_10_1534_g3_119_400724 crossref_primary_10_1038_s41587_022_01307_0 crossref_primary_10_1016_j_cub_2020_08_004 crossref_primary_10_1093_nar_gkad184 crossref_primary_10_1186_s13073_024_01352_1 crossref_primary_10_1371_journal_ppat_1004967 crossref_primary_10_1016_j_xcrm_2021_100349 crossref_primary_10_1038_nature22367 crossref_primary_10_1111_pce_14012 crossref_primary_10_1126_sciimmunol_abk0957 crossref_primary_10_1016_j_plaphy_2019_06_012 crossref_primary_10_1016_j_molcel_2023_04_002 crossref_primary_10_1093_bioadv_vbac097 crossref_primary_10_7717_peerj_5742 crossref_primary_10_1038_s41598_018_32146_2 crossref_primary_10_3390_jcm10163520 crossref_primary_10_1371_journal_pbio_3001826 crossref_primary_10_1186_s12864_016_2482_z crossref_primary_10_1038_s41586_024_08453_2 crossref_primary_10_3389_fimmu_2023_1108368 crossref_primary_10_1101_gr_258871_119 crossref_primary_10_7554_eLife_92393 crossref_primary_10_1016_j_cub_2023_07_022 crossref_primary_10_21105_joss_07012 crossref_primary_10_1371_journal_pcbi_1005244 crossref_primary_10_1093_plphys_kiaa012 crossref_primary_10_1371_journal_pone_0187243 crossref_primary_10_1093_jxb_erad347 crossref_primary_10_1111_pbi_13223 crossref_primary_10_1016_j_csbj_2024_09_017 crossref_primary_10_1038_s41588_018_0102_3 crossref_primary_10_1186_s12864_018_4469_4 crossref_primary_10_1186_s13059_019_1660_0 crossref_primary_10_1093_nar_gkac907 crossref_primary_10_1002_bies_201600028 crossref_primary_10_1093_nar_gkx358 crossref_primary_10_1093_nar_gkae095 crossref_primary_10_3390_jdb8040027 crossref_primary_10_1007_s11306_017_1203_1 crossref_primary_10_1093_insilicoplants_diab022 crossref_primary_10_1093_nar_gky681 crossref_primary_10_1016_j_xgen_2022_100232 crossref_primary_10_7554_eLife_53659 crossref_primary_10_1126_sciadv_add2911 crossref_primary_10_1186_s12915_021_00975_9 crossref_primary_10_1038_s41467_024_45706_0 crossref_primary_10_1007_s42994_024_00176_2 crossref_primary_10_1158_2159_8290_CD_20_1793 crossref_primary_10_3389_fgene_2024_1424085 crossref_primary_10_1186_s12860_021_00382_6 crossref_primary_10_1242_dev_199589 crossref_primary_10_7554_eLife_92393_3 crossref_primary_10_1093_bib_bbae306 crossref_primary_10_1038_s41596_022_00692_9 crossref_primary_10_3389_fpls_2024_1421503 crossref_primary_10_1038_leu_2017_116 crossref_primary_10_1093_bib_bbad250 crossref_primary_10_1093_nar_gkaa1057 crossref_primary_10_1093_bioinformatics_btw525 crossref_primary_10_1093_bioinformatics_bty703 crossref_primary_10_1093_nar_gkaa1055 crossref_primary_10_1038_ncomms8551 crossref_primary_10_3389_fmicb_2022_861528 crossref_primary_10_1371_journal_pcbi_1005449 crossref_primary_10_1016_j_neuron_2016_11_036 crossref_primary_10_1016_j_compbiolchem_2024_108077 crossref_primary_10_1038_s41386_024_01805_6 crossref_primary_10_1038_s41467_019_13888_7 crossref_primary_10_1155_2022_1027288 crossref_primary_10_1016_j_celrep_2022_111838 crossref_primary_10_1016_j_jad_2024_01_034 crossref_primary_10_1038_s41598_017_06099_x crossref_primary_10_1016_j_celrep_2021_109221 crossref_primary_10_3390_genes5041115 crossref_primary_10_1093_pnasnexus_pgad113 crossref_primary_10_1038_s41598_019_43767_6 crossref_primary_10_1038_s41586_018_0734_6 crossref_primary_10_1371_journal_pgen_1006120 crossref_primary_10_1093_eep_dvy020 crossref_primary_10_1016_j_csbj_2022_05_003 crossref_primary_10_1371_journal_pcbi_1004590 crossref_primary_10_1126_sciadv_aba3064 crossref_primary_10_1016_j_molcel_2023_03_001 crossref_primary_10_1038_s41598_019_52210_9 crossref_primary_10_1016_j_cell_2019_09_035 crossref_primary_10_1038_s41467_022_34276_8 crossref_primary_10_1038_s41467_021_23216_7 |
| Cites_doi | 10.1038/nature08800 10.1093/nar/gkr993 10.1126/science.1222794 10.1101/gr.1953904 10.1073/pnas.0903103106 10.1126/science.1136800 10.1073/pnas.1311818110 10.1093/nar/18.20.6097 10.1093/bioinformatics/bts202 10.1101/gr.094144.109 10.1093/nar/gkp950 10.1105/tpc.109.066647 10.1093/gbe/evq032 10.1016/j.ajhg.2013.01.002 10.1093/database/bar030 10.1105/tpc.111.084913 10.1093/nar/gkj143 10.1093/nar/gkn660 10.1038/nbt.1893 10.1093/bioinformatics/btq488 10.1093/bioinformatics/18.suppl_1.S96 10.1093/nar/gkn844 10.1038/msb.2011.75 10.1126/science.290.5493.972 10.1111/j.1574-6968.2008.01293.x 10.1093/nar/gks1221 10.1016/j.cell.2008.05.023 10.1038/nrg2641 10.1007/978-90-481-9069-0_3 10.1002/jcb.22077 10.1038/nbt.2486 10.1038/nature10414 10.1105/tpc.108.064048 10.1126/science.1162327 10.1101/gr.151472.112 10.1016/j.cell.2008.05.024 10.1093/nar/gkq1303 10.1074/jbc.M103097200 10.1073/pnas.89.16.7345 10.1371/journal.pone.0042779 10.1007/978-90-481-9069-0_7 10.1093/nar/gkq858 10.1101/gr.164327.113 10.1101/gr.5655606 10.1186/gb-2001-2-8-research0029 10.1007/978-90-481-9069-0_4 10.1007/978-90-481-9069-0_8 10.1093/nar/gkr070 10.1016/j.cell.2008.06.030 10.1093/bioinformatics/btn645 10.1093/nar/gkt890 10.1038/nature01554 10.1093/nar/gkn631 10.1038/nbt1246 10.1038/ng2117 10.1093/nar/gkr1012 10.1073/pnas.73.3.804 10.1093/bioinformatics/btr257 10.1016/j.cell.2013.07.034 10.1186/gb-2011-12-4-r34 10.1038/nature12311 10.1101/gr.085449.108 10.1038/nrg2845 10.1186/1471-2105-7-429 10.1093/nar/gkp985 10.1093/nar/gkh246 10.1186/gb-2002-3-12-research0087 10.1016/j.cell.2012.12.009 10.1016/S0021-9258(17)37118-1 |
| ContentType | Journal Article |
| Copyright | Copyright © 2014 Elsevier Inc. All rights reserved. 2014 Elsevier Inc. All rights reserved. 2014 |
| Copyright_xml | – notice: Copyright © 2014 Elsevier Inc. All rights reserved. – notice: 2014 Elsevier Inc. All rights reserved. 2014 |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6 5PM |
| DOI | 10.1016/j.cell.2014.08.009 |
| DatabaseName | 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 AGRICOLA MEDLINE - Academic |
| 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 | 1443 |
| ExternalDocumentID | PMC4163041 25215497 10_1016_j_cell_2014_08_009 |
| Genre | Research Support, U.S. Gov't, Non-P.H.S Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: CIHR grantid: MOP-77721 – fundername: NIGMS NIH HHS grantid: GM082971 – fundername: NICHD NIH HHS grantid: P01 HD039691 – fundername: NIGMS NIH HHS grantid: R01 GM082971 – fundername: NICHD NIH HHS grantid: P01 HD39691 – fundername: Howard Hughes Medical Institute |
| GroupedDBID | --- --K -DZ -ET -~X .-4 .55 .GJ .HR 0R~ 0WA 1CY 1RT 1VV 1~5 29B 2FS 2KS 2WC 3EH 3O- 4.4 457 4G. 53G 5GY 5RE 5VS 62- 6J9 6TJ 7-5 85S 9M8 AAEDT AAEDW AAFWJ AAHBH AAIKJ AAKRW AAKUH AALRI AAMRU AAQFI AAQXK AAVLU AAXUO AAYJJ AAYWO AAYXX ABCQX ABDGV ABDPE ABEFU ABJNI ABMAC ABOCM ABWVN ACGFO ACGFS ACNCT ACRPL ACVFH ADBBV ADCNI ADEZE ADMUD ADNMO ADVLN ADXHL AEFWE AENEX AETEA AEUPX AEXQZ AFPUW AFTJW AGCQF AGHFR AGHSJ AGKMS AGQPQ AHHHB AI. AIDAL AIGII AITUG AKAPO AKBMS AKRWK AKYEP ALMA_UNASSIGNED_HOLDINGS AMRAJ APXCP ASPBG AVWKF AZFZN BAWUL CITATION CS3 DIK DU5 E3Z EBS EJD F5P FCP FDB FEDTE FGOYB FIRID G-2 HH5 HVGLF HZ~ H~9 IH2 IHE IXB J1W JIG K-O KOO KQ8 L7B LX5 M3Z M41 MVM N9A O-L O9- OHT OK1 OMK OZT P2P PUQ R2- RIG RNS ROL RPZ SCP SDG SDP SES SSZ TAE TN5 TR2 TWZ UBW UHB UKR UPT VH1 WH7 X7M YYP YYQ YZZ ZCA ZGI ZHY ZKB ZY4 CGR CUY CVF ECM EFKBS EIF NPM 7X8 7S9 L.6 5PM |
| ID | FETCH-LOGICAL-c501t-42c1cf4a81a6870dd42a4bde5358a6e523f4b37c7f3f48f5a1d166ff004924143 |
| ISSN | 0092-8674 1097-4172 |
| IngestDate | Thu Aug 21 18:21:07 EDT 2025 Sun Sep 28 11:21:50 EDT 2025 Fri Sep 05 04:06:16 EDT 2025 Mon Jul 21 06:02:55 EDT 2025 Thu Apr 24 22:50:46 EDT 2025 Tue Jul 01 02:16:50 EDT 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 6 |
| Language | English |
| License | Copyright © 2014 Elsevier Inc. All rights reserved. |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c501t-42c1cf4a81a6870dd42a4bde5358a6e523f4b37c7f3f48f5a1d166ff004924143 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| OpenAccessLink | http://www.cell.com/article/S0092867414010368/pdf |
| PMID | 25215497 |
| PQID | 1561980354 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_4163041 proquest_miscellaneous_2000214111 proquest_miscellaneous_1561980354 pubmed_primary_25215497 crossref_primary_10_1016_j_cell_2014_08_009 crossref_citationtrail_10_1016_j_cell_2014_08_009 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2014-09-11 |
| PublicationDateYYYYMMDD | 2014-09-11 |
| PublicationDate_xml | – month: 09 year: 2014 text: 2014-09-11 day: 11 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Cell |
| PublicationTitleAlternate | Cell |
| PublicationYear | 2014 |
| References | Baldauf (10.1016/j.cell.2014.08.009_bib5) 2000; 290 Noyes (10.1016/j.cell.2014.08.009_bib42) 2008; 133 Persikov (10.1016/j.cell.2014.08.009_bib46) 2014; 42 Zhu (10.1016/j.cell.2014.08.009_bib64) 2011; 39 Park (10.1016/j.cell.2014.08.009_bib45) 2009; 10 Aurrecoechea (10.1016/j.cell.2014.08.009_bib65) 2009; 37 Gan (10.1016/j.cell.2014.08.009_bib23) 2011; 477 Maurano (10.1016/j.cell.2014.08.009_bib38) 2012; 337 Liu (10.1016/j.cell.2014.08.009_bib33) 2006; 16 Ray (10.1016/j.cell.2014.08.009_bib48) 2013; 499 Matys (10.1016/j.cell.2014.08.009_bib37) 2006; 34 Maglich (10.1016/j.cell.2014.08.009_bib34) 2001; 2 Schneider (10.1016/j.cell.2014.08.009_bib50) 1990; 18 Barski (10.1016/j.cell.2014.08.009_bib6) 2009; 107 Lang (10.1016/j.cell.2014.08.009_bib30) 2010; 2 Berger (10.1016/j.cell.2014.08.009_bib7) 2006; 24 Portales-Casamar (10.1016/j.cell.2014.08.009_bib47) 2010; 38 Lam (10.1016/j.cell.2014.08.009_bib29) 2011; 39 Rosenbloom (10.1016/j.cell.2014.08.009_bib49) 2012; 40 Shelest (10.1016/j.cell.2014.08.009_bib52) 2008; 286 Kulakovskiy (10.1016/j.cell.2014.08.009_bib70) 2010; 26 Yan (10.1016/j.cell.2014.08.009_bib61) 2013; 154 Jolma (10.1016/j.cell.2014.08.009_bib27) 2011; 52 Atwell (10.1016/j.cell.2014.08.009_bib3) 2010; 465 Sievers (10.1016/j.cell.2014.08.009_bib53) 2011; 7 Tanaka (10.1016/j.cell.2014.08.009_bib56) 2011; 27 Gordân (10.1016/j.cell.2014.08.009_bib24) 2009; 19 Fey (10.1016/j.cell.2014.08.009_bib66) 2009; 37 Weirauch (10.1016/j.cell.2014.08.009_bib59) 2013; 31 De Masi (10.1016/j.cell.2014.08.009_bib15) 2011; 39 Weirauch (10.1016/j.cell.2014.08.009_bib58) 2011; 52 de Mendoza (10.1016/j.cell.2014.08.009_bib16) 2013; 110 Finn (10.1016/j.cell.2014.08.009_bib20) 2010; 38 Wang (10.1016/j.cell.2014.08.009_bib57) 2013; 41 Frey (10.1016/j.cell.2014.08.009_bib67) 2007; 315 Eddy (10.1016/j.cell.2014.08.009_bib18) 2009; 23 Aggarwal (10.1016/j.cell.2014.08.009_bib1) 2010; 22 Carroll (10.1016/j.cell.2014.08.009_bib10) 2008; 134 Stormo (10.1016/j.cell.2014.08.009_bib54) 2010; 11 Bernard (10.1016/j.cell.2014.08.009_bib9) 2012; 7 Li (10.1016/j.cell.2014.08.009_bib32) 2011; 12 Galagan (10.1016/j.cell.2014.08.009_bib68) 2003; 422 Zhao (10.1016/j.cell.2014.08.009_bib63) 2011; 29 Desjarlais (10.1016/j.cell.2014.08.009_bib17) 1992; 89 Ohler (10.1016/j.cell.2014.08.009_bib44) 2002; 3 Alleyne (10.1016/j.cell.2014.08.009_bib2) 2009; 25 Newburger (10.1016/j.cell.2014.08.009_bib41) 2009; 37 Berger (10.1016/j.cell.2014.08.009_bib8) 2008; 133 FitzGerald (10.1016/j.cell.2014.08.009_bib21) 2004; 14 Badis (10.1016/j.cell.2014.08.009_bib4) 2009; 324 Enuameh (10.1016/j.cell.2014.08.009_bib19) 2013; 23 Christensen (10.1016/j.cell.2014.08.009_bib11) 2012; 28 Odom (10.1016/j.cell.2014.08.009_bib43) 2011; 52 Megraw (10.1016/j.cell.2014.08.009_bib39) 2009; 19 Mathias (10.1016/j.cell.2014.08.009_bib36) 2001; 276 Mariño-Ramírez (10.1016/j.cell.2014.08.009_bib35) 2004; 32 Mintseris (10.1016/j.cell.2014.08.009_bib40) 2006; 7 French (10.1016/j.cell.2014.08.009_bib22) 2013; 92 Stubbs (10.1016/j.cell.2014.08.009_bib55) 2011; 52 Yang (10.1016/j.cell.2014.08.009_bib62) 2011; 23 Cook (10.1016/j.cell.2014.08.009_bib12) 1994; 269 Seeman (10.1016/j.cell.2014.08.009_bib51) 1976; 73 de Boer (10.1016/j.cell.2014.08.009_bib14) 2014; 24 Huber (10.1016/j.cell.2014.08.009_bib26) 2002; 18 Jolma (10.1016/j.cell.2014.08.009_bib28) 2013; 152 Yamaguchi (10.1016/j.cell.2014.08.009_bib60) 2010; 22 Kinsella (10.1016/j.cell.2014.08.009_bib69) 2011; 2011 de Boer (10.1016/j.cell.2014.08.009_bib13) 2012; 40 Hindorff (10.1016/j.cell.2014.08.009_bib25) 2009; 106 Lee (10.1016/j.cell.2014.08.009_bib31) 2007; 39 |
| References_xml | – volume: 465 start-page: 627 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib3 article-title: Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines publication-title: Nature doi: 10.1038/nature08800 – volume: 40 start-page: D169 year: 2012 ident: 10.1016/j.cell.2014.08.009_bib13 article-title: YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr993 – volume: 337 start-page: 1190 year: 2012 ident: 10.1016/j.cell.2014.08.009_bib38 article-title: Systematic localization of common disease-associated variation in regulatory DNA publication-title: Science doi: 10.1126/science.1222794 – volume: 14 start-page: 1562 year: 2004 ident: 10.1016/j.cell.2014.08.009_bib21 article-title: Clustering of DNA sequences in human promoters publication-title: Genome Res. doi: 10.1101/gr.1953904 – volume: 106 start-page: 9362 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib25 article-title: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0903103106 – volume: 315 start-page: 972 year: 2007 ident: 10.1016/j.cell.2014.08.009_bib67 article-title: Clustering by passing messages between data points publication-title: Science doi: 10.1126/science.1136800 – volume: 110 start-page: E4858 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib16 article-title: Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1311818110 – volume: 18 start-page: 6097 year: 1990 ident: 10.1016/j.cell.2014.08.009_bib50 article-title: Sequence logos: a new way to display consensus sequences publication-title: Nucleic Acids Res. doi: 10.1093/nar/18.20.6097 – volume: 28 start-page: i84 year: 2012 ident: 10.1016/j.cell.2014.08.009_bib11 article-title: Recognition models to predict DNA-binding specificities of homeodomain proteins publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts202 – volume: 19 start-page: 2090 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib24 article-title: Distinguishing direct versus indirect transcription factor-DNA interactions publication-title: Genome Res. doi: 10.1101/gr.094144.109 – volume: 38 start-page: D105 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib47 article-title: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkp950 – volume: 22 start-page: 1174 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib1 article-title: Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis publication-title: Plant Cell doi: 10.1105/tpc.109.066647 – volume: 2 start-page: 488 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib30 article-title: Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evq032 – volume: 92 start-page: 489 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib22 article-title: Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers publication-title: Am. J. Hum. Genet. doi: 10.1016/j.ajhg.2013.01.002 – volume: 2011 start-page: bar030 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib69 article-title: Ensembl BioMarts: a hub for data retrieval across taxonomic space publication-title: Database (Oxford) doi: 10.1093/database/bar030 – volume: 23 start-page: 2155 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib62 article-title: The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes publication-title: Plant Cell doi: 10.1105/tpc.111.084913 – volume: 34 start-page: D108 year: 2006 ident: 10.1016/j.cell.2014.08.009_bib37 article-title: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkj143 – volume: 37 start-page: D77 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib41 article-title: UniPROBE: an online database of protein binding microarray data on protein-DNA interactions publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn660 – volume: 29 start-page: 480 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib63 article-title: Quantitative analysis demonstrates most transcription factors require only simple models of specificity publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1893 – volume: 26 start-page: 2622 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib70 article-title: Deep and wide digging for binding motifs in ChIP-Seq data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq488 – volume: 18 start-page: S96 issue: Suppl 1 year: 2002 ident: 10.1016/j.cell.2014.08.009_bib26 article-title: Variance stabilization applied to microarray data calibration and to the quantification of differential expression publication-title: Bioinformatics doi: 10.1093/bioinformatics/18.suppl_1.S96 – volume: 37 start-page: D515 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib66 article-title: dictyBase—a Dictyostelium bioinformatics resource update publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn844 – volume: 7 start-page: 539 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib53 article-title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega publication-title: Mol. Syst. Biol. doi: 10.1038/msb.2011.75 – volume: 290 start-page: 972 year: 2000 ident: 10.1016/j.cell.2014.08.009_bib5 article-title: A kingdom-level phylogeny of eukaryotes based on combined protein data publication-title: Science doi: 10.1126/science.290.5493.972 – volume: 286 start-page: 145 year: 2008 ident: 10.1016/j.cell.2014.08.009_bib52 article-title: Transcription factors in fungi publication-title: FEMS Microbiol. Lett. doi: 10.1111/j.1574-6968.2008.01293.x – volume: 41 start-page: D171 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib57 article-title: Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium publication-title: Nucleic Acids Res. doi: 10.1093/nar/gks1221 – volume: 23 start-page: 205 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib18 article-title: A new generation of homology search tools based on probabilistic inference publication-title: Genome Inform. – volume: 133 start-page: 1277 year: 2008 ident: 10.1016/j.cell.2014.08.009_bib42 article-title: Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites publication-title: Cell doi: 10.1016/j.cell.2008.05.023 – volume: 10 start-page: 669 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib45 article-title: ChIP-seq: advantages and challenges of a maturing technology publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2641 – volume: 52 start-page: 25 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib58 article-title: A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution publication-title: Subcell. Biochem. doi: 10.1007/978-90-481-9069-0_3 – volume: 107 start-page: 11 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib6 article-title: Genomic location analysis by ChIP-Seq publication-title: J. Cell. Biochem. doi: 10.1002/jcb.22077 – volume: 31 start-page: 126 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib59 article-title: Evaluation of methods for modeling transcription factor sequence specificity publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2486 – volume: 477 start-page: 419 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib23 article-title: Multiple reference genomes and transcriptomes for Arabidopsis thaliana publication-title: Nature doi: 10.1038/nature10414 – volume: 22 start-page: 1249 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib60 article-title: VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis publication-title: Plant Cell doi: 10.1105/tpc.108.064048 – volume: 324 start-page: 1720 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib4 article-title: Diversity and complexity in DNA recognition by transcription factors publication-title: Science doi: 10.1126/science.1162327 – volume: 23 start-page: 928 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib19 article-title: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants publication-title: Genome Res. doi: 10.1101/gr.151472.112 – volume: 133 start-page: 1266 year: 2008 ident: 10.1016/j.cell.2014.08.009_bib8 article-title: Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences publication-title: Cell doi: 10.1016/j.cell.2008.05.024 – volume: 39 start-page: 4680 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib29 article-title: Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq1303 – volume: 276 start-page: 32696 year: 2001 ident: 10.1016/j.cell.2014.08.009_bib36 article-title: Altering the DNA-binding specificity of the yeast Matalpha 2 homeodomain protein publication-title: J. Biol. Chem. doi: 10.1074/jbc.M103097200 – volume: 89 start-page: 7345 year: 1992 ident: 10.1016/j.cell.2014.08.009_bib17 article-title: Toward rules relating zinc finger protein sequences and DNA binding site preferences publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.89.16.7345 – volume: 7 start-page: e42779 year: 2012 ident: 10.1016/j.cell.2014.08.009_bib9 article-title: Increasing coverage of transcription factor position weight matrices through domain-level homology publication-title: PLoS ONE doi: 10.1371/journal.pone.0042779 – volume: 52 start-page: 155 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib27 article-title: Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro publication-title: Subcell. Biochem. doi: 10.1007/978-90-481-9069-0_7 – volume: 39 start-page: D111 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib64 article-title: FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq858 – volume: 24 start-page: 154 year: 2014 ident: 10.1016/j.cell.2014.08.009_bib14 article-title: A unified model for yeast transcript definition publication-title: Genome Res. doi: 10.1101/gr.164327.113 – volume: 16 start-page: 1517 year: 2006 ident: 10.1016/j.cell.2014.08.009_bib33 article-title: Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection publication-title: Genome Res. doi: 10.1101/gr.5655606 – volume: 2 year: 2001 ident: 10.1016/j.cell.2014.08.009_bib34 article-title: Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes publication-title: Genome Biol. doi: 10.1186/gb-2001-2-8-research0029 – volume: 52 start-page: 75 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib55 article-title: Function and Evolution of C2H2 Zinc Finger Arrays publication-title: Subcell. Biochem. doi: 10.1007/978-90-481-9069-0_4 – volume: 52 start-page: 175 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib43 article-title: Identification of Transcription Factor-DNA Interactions In Vivo publication-title: Subcell. Biochem. doi: 10.1007/978-90-481-9069-0_8 – volume: 39 start-page: 4553 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib15 article-title: Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr070 – volume: 134 start-page: 25 year: 2008 ident: 10.1016/j.cell.2014.08.009_bib10 article-title: Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution publication-title: Cell doi: 10.1016/j.cell.2008.06.030 – volume: 25 start-page: 1012 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib2 article-title: Predicting the binding preference of transcription factors to individual DNA k-mers publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn645 – volume: 42 start-page: 97 year: 2014 ident: 10.1016/j.cell.2014.08.009_bib46 article-title: De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkt890 – volume: 422 start-page: 859 year: 2003 ident: 10.1016/j.cell.2014.08.009_bib68 article-title: The genome sequence of the filamentous fungus Neurospora crassa publication-title: Nature doi: 10.1038/nature01554 – volume: 37 start-page: D526 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib65 article-title: GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkn631 – volume: 24 start-page: 1429 year: 2006 ident: 10.1016/j.cell.2014.08.009_bib7 article-title: Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities publication-title: Nat. Biotechnol. doi: 10.1038/nbt1246 – volume: 39 start-page: 1235 year: 2007 ident: 10.1016/j.cell.2014.08.009_bib31 article-title: A high-resolution atlas of nucleosome occupancy in yeast publication-title: Nat. Genet. doi: 10.1038/ng2117 – volume: 40 start-page: D912 year: 2012 ident: 10.1016/j.cell.2014.08.009_bib49 article-title: ENCODE whole-genome data in the UCSC Genome Browser: update 2012 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr1012 – volume: 73 start-page: 804 year: 1976 ident: 10.1016/j.cell.2014.08.009_bib51 article-title: Sequence-specific recognition of double helical nucleic acids by proteins publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.73.3.804 – volume: 27 start-page: 1603 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib56 article-title: Improved similarity scores for comparing motifs publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr257 – volume: 154 start-page: 801 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib61 article-title: Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites publication-title: Cell doi: 10.1016/j.cell.2013.07.034 – volume: 12 start-page: R34 year: 2011 ident: 10.1016/j.cell.2014.08.009_bib32 article-title: The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding publication-title: Genome Biol. doi: 10.1186/gb-2011-12-4-r34 – volume: 499 start-page: 172 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib48 article-title: A compendium of RNA-binding motifs for decoding gene regulation publication-title: Nature doi: 10.1038/nature12311 – volume: 19 start-page: 644 year: 2009 ident: 10.1016/j.cell.2014.08.009_bib39 article-title: A transcription factor affinity-based code for mammalian transcription initiation publication-title: Genome Res. doi: 10.1101/gr.085449.108 – volume: 11 start-page: 751 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib54 article-title: Determining the specificity of protein-DNA interactions publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2845 – volume: 7 start-page: 429 year: 2006 ident: 10.1016/j.cell.2014.08.009_bib40 article-title: Design of a combinatorial DNA microarray for protein-DNA interaction studies publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-429 – volume: 38 start-page: D211 year: 2010 ident: 10.1016/j.cell.2014.08.009_bib20 article-title: The Pfam protein families database publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkp985 – volume: 32 start-page: 949 year: 2004 ident: 10.1016/j.cell.2014.08.009_bib35 article-title: Statistical analysis of over-represented words in human promoter sequences publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh246 – volume: 3 year: 2002 ident: 10.1016/j.cell.2014.08.009_bib44 article-title: Computational analysis of core promoters in the Drosophila genome publication-title: Genome Biol. doi: 10.1186/gb-2002-3-12-research0087 – volume: 152 start-page: 327 year: 2013 ident: 10.1016/j.cell.2014.08.009_bib28 article-title: DNA-binding specificities of human transcription factors publication-title: Cell doi: 10.1016/j.cell.2012.12.009 – volume: 269 start-page: 9374 year: 1994 ident: 10.1016/j.cell.2014.08.009_bib12 article-title: Mutations in the zinc-finger region of the yeast regulatory protein ADR1 affect both DNA binding and transcriptional activation publication-title: J. Biol. Chem. doi: 10.1016/S0021-9258(17)37118-1 |
| SSID | ssj0008555 |
| Score | 2.6578424 |
| Snippet | Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling... Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ~1% of all eukaryotic TFs. Broadly... |
| SourceID | pubmedcentral proquest pubmed crossref |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | 1431 |
| SubjectTerms | alleles Arabidopsis Arabidopsis - genetics Arabidopsis - metabolism binding sites chromatin Chromatin Immunoprecipitation DNA DNA-binding domains eukaryotic cells gene regulatory networks human diseases Humans Nucleotide Motifs Polymorphism, Single Nucleotide precipitin tests Promoter Regions, Genetic Protein Binding Quantitative Trait Loci risk Sequence Analysis, DNA single nucleotide polymorphism transcription factors Transcription Factors - metabolism |
| Title | Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/25215497 https://www.proquest.com/docview/1561980354 https://www.proquest.com/docview/2000214111 https://pubmed.ncbi.nlm.nih.gov/PMC4163041 |
| Volume | 158 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwELagCIkL4s2Wh4zErUoVO3Yex1XpqoVSDuyK5RQ5TqxuWSXVkj20v55x_EjSAipcoij2riPPZDxjfzMfQu8JL7iIwjBIU0YDsH40EJKwoFIyrggXiexq6X0-jY8W7OOSLx0lvM0uaYt9efXbvJL_kSo8A7nqLNl_kKz_U3gA9yBfuIKE4XorGX9wWJbWgYqPXf5ehxjc_hCby0aXZO2WJG8gZh3JDtgJA6M2JPS6lEQ7OuQ9qNYef_GtWm3E1vBGWY7wHl_93W46T9c9OFTv_Rtc_plY-ZOOxrDxTVt4aUvrZbccQHKaMoEMzWgGZjQ29DrejPJ07wIMb0QCCNKigVHUzwYLrGu9YbzNPsL5vj6y0KA71hVXDbN-qXLH86df8tni5CSfHy7nd9E9moDfpB3i409-FU45N-wV9lVtwpTB9l0fYeyU3Ig0rgNmBx7I_BF6aEMHPDV68Bjdqeon6L4hE718ir6OtAGDNmCvDbhRuNcGPNIGbLQBO23AA214hhazw_nBUWApMwLJQ9IGjEoiFRMpETFY4rJkVLCirHjEUxFXnEaKFVEiEwU3qeKClCSOldKBIvhyLHqOduqmrl4izFWc0SSLKUTQTBWZSLXrTwupYBIVLyeIuDnLpa0nr2lN1rkDDp7nep5zPc-55joNswna87-5MNVU_tr7nRNFDkZPN4u6arY_cwJef5aGEWd_7qNz0ChhsJZP0AsjPj8mBaeVsyyZoGQkWN9BF10ft9Srs674ug5gQkZ2bzHuK_Sg_3peo512s63egAvbFm87Xf0FQVWbgg |
| linkProvider | Flying Publisher |
| 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=Determination+and+Inference+of+Eukaryotic+Transcription+Factor+Sequence+Specificity&rft.jtitle=Cell&rft.au=Weirauch%2C+Matthew+T&rft.au=Yang%2C+Ally&rft.au=Albu%2C+Mihai&rft.au=Cote%2C+Atina+G&rft.date=2014-09-11&rft.issn=0092-8674&rft.volume=158+p.1431-1443&rft.spage=1431&rft.epage=1443&rft_id=info:doi/10.1016%2Fj.cell.2014.08.009&rft.externalDBID=NO_FULL_TEXT |
| 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 |