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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W247-52. doi: 10.1093/nar/gkp464. Epub 2009 May 31.

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

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1
Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy.

Abstract

The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time. The website is free and open to all users and there is no login requirement. Address: http://www.beaconlab.it/pscan.

PMID:
19487240
PMCID:
PMC2703934
DOI:
10.1093/nar/gkp464
[Indexed for MEDLINE]
Free PMC Article
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