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COUGER-co-factors associated with uniquely-bound genomic regions

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Item Type:Article
Title:COUGER-co-factors associated with uniquely-bound genomic regions
Creators Name:Munteanu, A. and Ohler, U. and Gordân, R.
Abstract:Most transcription factors (TFs) belong to protein families that share a common DNA binding domain and have very similar DNA binding preferences. However, many paralogous TFs (i.e. members of the same TF family) perform different regulatory functions and interact with different genomic regions in the cell. A potential mechanism for achieving this differential in vivo specificity is through interactions with protein co-factors. Computational tools for studying the genomic binding profiles of paralogous TFs and identifying their putative co-factors are currently lacking. Here, we present an interactive web implementation of COUGER, a classification-based framework for identifying protein co-factors that might provide specificity to paralogous TFs. COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences. To achieve this task, COUGER uses a classification approach, with features that reflect the DNA-binding specificities of the putative co-factors. The identified co-factors are presented in a user-friendly output page, together with information that allows the user to understand and to explore the contributions of individual co-factor features. COUGER can be run as a stand-alone tool or through a web interface: http://couger.oit.duke.edu.
Keywords:Binding Sites, DNA-Binding Proteins, Genomics, Internet, Software, Transcription Factors
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:42
Number:Web Server issue
Page Range:W461-W467
Date:July 2014
Official Publication:https://doi.org/10.1093/nar/gku435
PubMed:View item in PubMed

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