ZOOLOGICAL RESEARCH 2012, 33(E5-6) 121-128 DOI:   10.3724/SP.J.1141.2012.E05-06E121   ISSN: 0254-5853 CN: 53-1040/Q

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Keywords
ChIP-seq
Bayesian
Peak calling
Gene regulation
Authors
Yanfeng ZHANG
Bing SU
PubMed
Article by Yanfeng ZHANG
Article by Bing SU

Peak identification for ChIP-seq data with no controls

Yanfeng ZHANG, Bing SU

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is increasingly being used for genome-wide profiling of transcriptional regulation, as this technique enables dissection of the gene regulatory networks. With input as control, a variety of statistical methods have been proposed for identifying the enriched regions in the genome, i.e., the transcriptional factor binding sites and chromatin modifications. However, when there are no controls, whether peak calling is still reliable awaits systematic evaluations. To address this question, we used a Bayesian framework approach to show the effectiveness of peak calling without controls (PCWC). Using several different types of ChIP-seq data, we demonstrated the relatively high accuracy of PCWC with less than a 5% false discovery rate (FDR). Compared with previously published methods, e.g., the model-based analysis of ChIP-seq (MACS), PCWC is reliable with lower FDR. Furthermore, to interpret the biological significance of the called peaks, in combination with microarray gene expression data, gene ontology annotation and subsequent motif discovery, our results indicate PCWC possesses a high efficiency. Additionally, using in silico data, only a small number of peaks were identified, suggesting the significantly low FDR for PCWC.

Keywords ChIP-seq   Bayesian   Peak calling   Gene regulation  
Received 2012-09-06 Revised 2012-10-31 Online:  
DOI: 10.3724/SP.J.1141.2012.E05-06E121
Fund:

This study was supported by the National 973 project of China (2011CBA01101) and the National Natural Science Foundation of China (30871343 and 31130051)

Corresponding Authors:
Email: sub@mail.kiz.ac.cn
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