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This article is part of the supplement: 22nd International Conference on Genome Informatics: Systems Biology

Open Access Proceedings

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite

Xi Wang12 and Xuegong Zhang1*

Author Affiliations

1 MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China

2 Current address: School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan NSW 2308, Australia

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BMC Systems Biology 2011, 5(Suppl 2):S3  doi:10.1186/1752-0509-5-S2-S3

Published: 14 December 2011

Abstract

Background

Chromatin immunoprecipitation combined with the next-generation DNA sequencing technologies (ChIP-seq) becomes a key approach for detecting genome-wide sets of genomic sites bound by proteins, such as transcription factors (TFs). Several methods and open-source tools have been developed to analyze ChIP-seq data. However, most of them are designed for detecting TF binding regions instead of accurately locating transcription factor binding sites (TFBSs). It is still challenging to pinpoint TFBSs directly from ChIP-seq data, especially in regions with closely spaced binding events.

Results

With the aim to pinpoint TFBSs at a high resolution, we propose a novel method named SeqSite, implementing a two-step strategy: detecting tag-enriched regions first and pinpointing binding sites in the detected regions. The second step is done by modeling the tag density profile, locating TFBSs on each strand with a least-squares model fitting strategy, and merging the detections from the two strands. Experiments on simulation data show that SeqSite can locate most of the binding sites more than 40-bp from each other. Applications on three human TF ChIP-seq datasets demonstrate the advantage of SeqSite for its higher resolution in pinpointing binding sites compared with existing methods.

Conclusions

We have developed a computational tool named SeqSite, which can pinpoint both closely spaced and isolated binding sites, and consequently improves the resolution of TFBS detection from ChIP-seq data.