title: COUGER--co-factors associated with uniquely-bound genomic regions.
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.
authors.affiliation: Faculty of Computer Science, Alexandru I. Cuza University, Iasi 700483, Romania Berlin Institute for Medical Systems Biology, Max Delbruck Center, 13125 Berlin, Germany.
authors.forename: Alina
authors.initials: A
authors.lastname: Munteanu
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbruck Center, 13125 Berlin, Germany Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA.
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
authors.affiliation: Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA raluca.gordan@duke.edu.
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D023281:Genomics; D020407:Internet; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors