title: Detection of interacting transcription factors in human tissues using predicted DNA binding affinity.
abstract: BACKGROUND
  Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF.
  
  
  RESULTS
  We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue.
  
  
  CONCLUSIONS
  The findings from this study indicate that tissue-specific gene expression is regulated by one or two central regulators and a large number of TFs interacting with these central hubs. Our results are in agreement with recent experimental studies.
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany. mysickov@molgen.mpg.de
authors.forename: Alena
authors.initials: A
authors.lastname: Myšičková
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D005786:Gene Expression Regulation; D006801:Humans; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA