ChromBiSim: Interactive chromatin biclustering using a simple approach
Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combi...
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| Published in | Genomics (San Diego, Calif.) Vol. 109; no. 5-6; pp. 353 - 361 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.10.2017
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0888-7543 1089-8646 1089-8646 |
| DOI | 10.1016/j.ygeno.2017.05.010 |
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| Abstract | Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis.
ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species.
ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages.
•ChromBiSim is an interactive GUI based tool.•It is the very first unsupervised biclustering tool for mining histone modifications combinations.•It mines all possible combinations of histone modifications and is based on binarization approach.•Useful for comparative analysis of epigenomic profiles based on present signals of histone modifications. |
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| AbstractList | Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis.
ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species.
ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages.
•ChromBiSim is an interactive GUI based tool.•It is the very first unsupervised biclustering tool for mining histone modifications combinations.•It mines all possible combinations of histone modifications and is based on binarization approach.•Useful for comparative analysis of epigenomic profiles based on present signals of histone modifications. Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis.ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species.ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species. ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species.Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species.ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages.AVAILABILITYChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. |
| Author | Noureen, Nighat Fazal, Sahar Zohaib, Hafiz Muhammad Qadir, Muhammad Abdul |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28579515$$D View this record in MEDLINE/PubMed |
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| Keywords | Local patterns Genome wide histone marks Binarization approach Histone code hypothesis Biclusters |
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| SubjectTerms | Algorithms Biclusters Binarization approach chromatin Chromatin - genetics Cluster Analysis Computational Biology - methods Data Mining Epigenomics - methods genome Genome wide histone marks heat HeLa Cells Histone Code Histone code hypothesis histones Histones - chemistry Humans K562 Cells Local patterns user interface |
| Title | ChromBiSim: Interactive chromatin biclustering using a simple approach |
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