A distance difference matrix approach to identifying transcription factors that regulate differential gene expression.
We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression.
De Bleser
Pieter
P
Bioinformatics Core, VIB, B-9052 Ghent, Belgium. pieterdb@dmbr.UGent.be
Hooghe
Bart
B
Vlieghe
Dominique
D
van Roy
Frans
F
D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D014157:Transcription Factors