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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Lihua J Zhu12*, Claude Gazin3, Nathan D Lawson12, Hervé Pagès4, Simon M Lin5, David S Lapointe6 and Michael R Green12

Author Affiliations

1 Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA

2 Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA

3 UMR217 CNRS/CEA, iRCM-CEA, Evry, Ile de France 91057, France

4 Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109-1024, USA

5 The Biomedical Informatics Center, Northwestern University, Chicago IL 60611, USA

6 Information Services, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA

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BMC Bioinformatics 2010, 11:237  doi:10.1186/1471-2105-11-237

Published: 11 May 2010

Abstract

Background

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.

Results

We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes.

Conclusions

ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database.