DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.

ABSTRACT:

Motivation

Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct 'footprint' patterns at binding sites. Nearly all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites. Additionally, a comprehensive and systematic comparison of footprinting methods for specifically identifying which motif sites for a specific factor are bound has not been performed.

Results

Using DNase-seq data fro

SUBMITTER: Quach B 

PROVIDER: S-EPMC6075477 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature