Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
نویسندگان
چکیده
منابع مشابه
Nebula - a web-server for advanced ChIP-seq data analysis
MOTIVATION ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. RESULTS N...
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Summary: High-throughput sequencing technologies such as ChIPseq have deepened our understanding in many biological processes. De novo motif search is one of the key downstream computational analysis following the ChIP-seq experiments and several algorithms have been proposed for this purpose. However, most webbased systems do not perform independent filtering or enrichment analyses to ensure t...
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4 The k-mean alignment algorithm and the cluster_peak method 9 4.1 Definition of weight in the distance function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 4.2 The cluster_peak method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.3 The choice of the final classification with the bending index and the Silhouette plot . . . . . . ...
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Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with the presence of one or more peaks and b...
متن کاملhmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data
UNLABELLED hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual sa...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2019
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkz332