PT  - JOURNAL ARTICLE
AU  - Zhong Wang
AU  - Andre L. Martins
AU  - Charles G. Danko
TI  - RTFBSDB: an integrated framework for transcription factor binding site analysis
AID  - 10.1101/036053
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 036053
4099  - http://biorxiv.org/content/early/2016/01/05/036053.short
4100  - http://biorxiv.org/content/early/2016/01/05/036053.full
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).