A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.

Genome biology ·Vol. 10 ·No. 12 ·2009-00-00 ·Pages R142

Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE

Abstract

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.

MeSH Terms

Binding Sites/genetics Chromatin Immunoprecipitation/statistics & numerical data Computational Biology/methods Humans Mycobacterium tuberculosis/genetics Software Transcription Factors/genetics,metabolism

Chemicals

Transcription Factors

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Lun Desmond S

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

Weiner Brian

Sherman David R

Galagan James E

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Article Info

Journal

Genome biology

Abbr.

Genome Biol

ISSN

1474-760X

DOI

10.1186/gb-2009-10-12-r142

desmond.lun@unisa.edu.au

Published

2009-00-00

Epub

2009-00-22

Pages

R142

Language

English

Region

England

NLM ID

100960660

PMCID

PMC2812949

Subset

External Links

PubMed source DOI: 10.1186/gb-2009-10-12-r142 PMC Full Text View journal details

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A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.

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