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We are analyzing https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-237.

Title:
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data | BMC Bioinformatics | Full Text
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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sites, pubmed, package, data, article, annotation, peaks, binding, gene, google, scholar, figure, chippeakanno, nearest, replicates, file, analysis, biological, chipseq, enriched, overlapping, chipchip, regions, transcription, yeast, central, bioconductor, bioinformatics, identified, genome, overlap, stebinding, function, list, cas, authors, packages, bmc, putative, tss, genes, generated, start, merged, site, users, original, software, chip, shows,

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springer nature background chip author information authors putative stat1-binding regions vivo protein-dna interactions putative cse4-binding sites availability modeling protein-dna interactions putative ste12-binding sites full size image authors scientific editing stat1-binding sites relative cse4-binding sites relative annotated cse4-binding sites ste12-binding sites merged high-throughput sequence data hypergeometric test phyper identify gene ontology gene ontology consortium ste12-binding sites relative org/packages/release/data/annotation/ annotated ste12-binding sites nature genetics 2000 standard high-throughput technologies hypergeometric test shows pair-wise comparisons transcription start site motif discovery motif discovery [3 privacy choices/manage cookies organism-specific bsgenome package analyzing chip-chip readouts massively parallel sequencing smyth gk high-throughput sequencing authors’ original file peak-calling software produces zhang zd facilitates batch annotation transcription start sites download stat1 dna association chip-seq experiments relative chip-chip analysis packages facilitate batch annotation dna-binding sites open software development biomedical informatics center drawing venn diagrams stat1-binding sites

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