RTFBSDB: an integrated framework for transcription factor binding site analysis

Abstract

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 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 and implementation: rtfbsdb available at (https://github.com/Danko-Lab/rtfbs_db).

Contact: dankoc@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Schematic illustrating the rtfbsdb workflow. Motifs are loaded into a CisBP.db object in R using an automated web scraper that imports data directly from the Cis-BP database. The set of motifs is reduced to those most applicable for analysis (right side) by removing TFs that are not expressed in the cell system of interest, and subsequently grouping motifs recognizing similar DNA sequences by clustering. The final set of motifs can be used to complete several common tasks in genomics (bottom row), including testing a set of DNA sequences for enriched motifs, scanning a target genome, or visualizing motifs as sequence logos