RT Journal Article
SR Electronic
T1 RTFBSDB: an integrated framework for transcription factor binding site analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 036053
DO 10.1101/036053
A1 Zhong Wang
A1 Andre L. Martins
A1 Charles G. Danko
YR 2016
UL http://biorxiv.org/content/early/2016/01/05/036053.abstract
AB Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here we introduce rtfbsdb, a unified framework that integrates a database of more than 65,000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.Availability: rtfbsdb is available via github (https://github.com/Danko-Lab/rtfbsdb).