We are analyzing https://link.springer.com/article/10.1186/1471-2105-11-237.

Title:
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data | BMC Bioinformatics
Description:
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 BSgenom e, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database.
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Keywords {🔍}

sites, pubmed, data, package, article, annotation, peaks, binding, gene, google, scholar, figure, chippeakanno, nearest, replicates, analysis, biological, file, chipseq, enriched, overlapping, chipchip, regions, transcription, yeast, bioconductor, central, identified, bioinformatics, genome, overlap, stebinding, function, list, cas, packages, putative, tss, genes, generated, start, merged, authors, site, software, users, find, full, chip, shows,

Topics {✒️}

vivo protein-dna interactions putative stat1-binding regions modeling protein-dna interactions putative cse4-binding sites high-throughput sequence data article download pdf putative ste12-binding sites stat1-binding sites relative full size image cse4-binding sites relative annotated cse4-binding sites ste12-binding sites merged org/packages/release/data/annotation/ ste12-binding sites relative analyzing chip-chip readouts annotated ste12-binding sites standard high-throughput technologies pair-wise comparisons organism-specific bsgenome package related subjects open software development massively parallel sequencing smyth gk high-throughput sequencing chip-chip analysis packages stat1 dna association dna-binding sites peak-calling software produces facilitates batch annotation feature-based approach privacy choices/manage cookies zhang zd chip-seq experiments relative facilitate batch annotation predefined dna targets stat1-binding sites modeling chip sequencing umms academic research efficient yeast chip-seq open-access cse4 binding-sites cse4-binding sites authors’ original file solexa sequencing data hypergeometric test phyper identify gene ontology gene ontology consortium biomed central binding sites annotated binding sites identified

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