Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
By F. Zambelli, Graziano Pesole, Giulio Pavesi. Nucleic Acids Res., 2009
414 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/4c8fc15267015bf81bc2ce9fb41a1a831498eac1
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Citations in the corpus
- iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, methodology): “iRegulon was compared to eight other publicly available motif enrichment tools, namely OPOSSUM [117], DIRE [80,112], PASTAA [32,113], PSCAN [114], Clover [16], AME [118], Allegro [115] and HOMER2 [116] (in the case of Homer2, de novo and known motif discovery are performed simultaneously but we cons”
- Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population (2012, methodology): “To search for an enrichment of DNA binding motifs in the set of 435 a-DMR genes, we used PSCAN”