A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.
We present CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows closely-spaced binding sites to be called accurately. We apply CSDeconv to novel ChIP-seq data for DosR binding in Mycobacterium tuberculosis and to existing data for GABP in humans and show that it can discriminate binding sites separated by as few as 40 bp.
Lun
Desmond S
DS
Phenomics and Bioinformatics Research Centre, School of Mathematics and Statistics, and Australian Centre for Plant Functional Genomics, University of South Australia, Mawson Lakes Boulevard, Mawson Lakes, SA 5095, Australia. desmond.lun@unisa.edu.au
Sherrid
Ashley
A
Weiner
Brian
B
Sherman
David R
DR
Galagan
James E
JE
D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000706:statistics & numerical data*; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D014157:Transcription Factors