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Open Access Highly Accessed Software

ChIPseek, a web-based analysis tool for ChIP data

Ting-Wen Chen12, Hsin-Pai Li134, Chi-Ching Lee12, Ruei-Chi Gan125, Po-Jung Huang12, Timothy H Wu6, Cheng-Yang Lee12, Yi-Feng Chang16 and Petrus Tang123*

Author Affiliations

1 Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan

2 Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan

3 Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan

4 Department of Microbiology and Immunology, Medical School of Chang Gung University, Taoyuan, Taiwan

5 Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan

6 Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan

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BMC Genomics 2014, 15:539  doi:10.1186/1471-2164-15-539

Published: 30 June 2014

Abstract

Background

Chromatin is a dynamic but highly regulated structure. DNA-binding proteins such as transcription factors, epigenetic and chromatin modifiers are responsible for regulating specific gene expression pattern and may result in different phenotypes. To reveal the identity of the proteins associated with the specific region on DNA, chromatin immunoprecipitation (ChIP) is the most widely used technique. ChIP assay followed by next generation sequencing (ChIP-seq) or microarray (ChIP-chip) is often used to study patterns of protein-binding profiles in different cell types and in cancer samples on a genome-wide scale. However, only a limited number of bioinformatics tools are available for ChIP datasets analysis.

Results

We present ChIPseek, a web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses. ChIPseek can provide statistical summary of the dataset including histogram of peak length distribution, histogram of distances to the nearest transcription start site (TSS), and pie chart (or bar chart) of genomic locations for users to have a comprehensive view on the dataset for further analysis. For examining the potential functions of peaks, ChIPseek provides peak annotation, visualization of peak genomic location, motif identification, sequence extraction, and comparison between datasets. Beyond that, ChIPseek also offers users the flexibility to filter peaks and re-analyze the filtered subset of peaks. ChIPseek supports 20 different genome assemblies for 12 model organisms including human, mouse, rat, worm, fly, frog, zebrafish, chicken, yeast, fission yeast, Arabidopsis, and rice. We use demo datasets to demonstrate the usage and intuitive user interface of ChIPseek.

Conclusions

ChIPseek provides a user-friendly interface for biologists to analyze large-scale ChIP data without requiring any programing skills. All the results and figures produced by ChIPseek can be downloaded for further analysis. The analysis tools built into ChIPseek, especially the ones for selecting and examine a subset of peaks from ChIP data, provides invaluable helps for exploring the high through-put data from either ChIP-seq or ChIP-chip. ChIPseek is freely available at http://chipseek.cgu.edu.tw webcite.

Keywords:
ChIP-seq; ChIP-chip; Analysis tool; Web-services; Peak annotation; Motif identification; Filter tools; Comparison