ChromBiSim: Interactive chromatin biclustering using a simple approach

• Published in: Genomics (San Diego, Calif.) Vol. 109; no. 5-6; pp. 353 - 361
• Main Authors: Noureen, Nighat, Zohaib, Hafiz Muhammad, Qadir, Muhammad Abdul, Fazal, Sahar
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2017
• Subjects: 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; Local patterns; Genome wide histone marks; Binarization approach; Histone code hypothesis; Biclusters
• ISSN: 0888-7543; 1089-8646; 1089-8646
• DOI: 10.1016/j.ygeno.2017.05.010

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.