Analyzing multiple data sets by interconnecting rsat programs via soap web services—an example with chip-chip data

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. Access through your institution Buy or

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services. _Nucleic Acids Res._ 34, W729–W732 (2006). Article  CAS  Google Scholar  Download references ACKNOWLEDGEMENTS This work was supported by the BioSapiens Network of Excellence funded

under the sixth Framework program of the European Communities (LSHG-CT-2003-503265) (O.S. postdoc grant, E.V. research fellowship), the Vrije Universiteit Brussel (Geconcerteerde

Onderzoeksactie 29) (M.T.-C. PhD grant) and by the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office, project P6/25 (BioMaGNet).

AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Bruxelles, Boulevard du

Triomphe, B-1050, Belgium Olivier Sand, Morgane Thomas-Chollier, Eric Vervisch & Jacques van Helden Authors * Olivier Sand View author publications You can also search for this author

inPubMed Google Scholar * Morgane Thomas-Chollier View author publications You can also search for this author inPubMed Google Scholar * Eric Vervisch View author publications You can also

search for this author inPubMed Google Scholar * Jacques van Helden View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence

to Jacques van Helden. SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIGURE 1 Full version of the feature map showing the positions of the significant hexanucleotides found in promoters of genes

from the BAS1_YPD cluster. (PDF 82 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Sand, O., Thomas-Chollier, M., Vervisch, E. _et al._ Analyzing

multiple data sets by interconnecting RSAT programs via SOAP Web services—an example with ChIP-chip data. _Nat Protoc_ 3, 1604–1615 (2008). https://doi.org/10.1038/nprot.2008.99 Download

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