title: C2Analyzer: Co-target-co-function analyzer.
abstract: MicroRNAs (miRNAs) interact with their target mRNAs and regulate biological processes at post-transcriptional level. While one miRNA can target many mRNAs, a single mRNA can also be targeted by a set of miRNAs. The targeted mRNAs may be involved in different biological processes that are described by gene ontology (GO) terms. The major challenges involved in analyzing these multitude regulations include identification of the combinatorial regulation of miRNAs as well as determination of the co-functionally-enriched miRNA pairs. The C2Analyzer: Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched. For a given set of GO term(s), it can also identify the set of miRNAs whose targets are enriched in the given GO term(s). Moreover, C2Analyzer can also identify the co-targeting miRNA pairs, their targets and GO processes, which they are involved in. The miRNA-miRNA co-functional relationship can also be saved as a .txt file, which can be used to further visualize the co-functional network by using other software like Cytoscape. C2Analyzer is freely available at www.bioinformatics.org/c2analyzer.
authors.affiliation: West Bengal University of Technology, Kolkata 700064, India.
authors.forename: Md
authors.initials: M
authors.lastname: Aftabuddin
authors.affiliation: Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India.
authors.forename: Chittabrata
authors.initials: C
authors.lastname: Mal
authors.affiliation: Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India.
authors.forename: Arindam
authors.initials: A
authors.lastname: Deb
authors.affiliation: Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India. Electronic address: skbmbg@caluniv.ac.in.
authors.forename: Sudip
authors.initials: S
authors.lastname: Kundu
mesh_terms: D020029:Base Pairing; D019295:Computational Biology / Q000379:methods*; D044127:Epigenesis, Genetic; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Co-function; Co-target; Gene ontology; MicroRNA; Post-transcriptional regulation