Introduction

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.

Publications

  1. COUGER--co-factors associated with uniquely-bound genomic regions.
    Cite this
    Munteanu A, Ohler U, Gordân R, 2014-07-01 - Nucleic acids research

Credits

  1. Alina Munteanu
    Developer

    Faculty of Computer Science, Alexandru I. Cuza University, Germany

  2. Uwe Ohler
    Developer

    Berlin Institute for Medical Systems Biology, Max Delbruck Center, United States of America

  3. Raluca Gordân
    Investigator

    Department of Biostatistics and Bioinformatics, Duke University

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006989
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByRaluca Gordân