Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services—an example with ChIP-chip data View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2008-09-18

AUTHORS

Olivier Sand, Morgane Thomas-Chollier, Eric Vervisch, Jacques van Helden

ABSTRACT

This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is ∼6 min on the example data set. More... »

PAGES

1604-1615

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nprot.2008.99

DOI

http://dx.doi.org/10.1038/nprot.2008.99

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1051387433

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18802441


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