Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
Open accessAbstract
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.
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Pscan and PASTAA identified transcription factors that may coordinate the changes in protein levels in apoE4-expressing cells.
“To determine which regulatory pathways help compensate for apoE4-induced mitochondrial dysfunction, we used Pscan [64] and PASTAA [63] to identify transcription factors that may coordinate the changes in protein levels in apoE4-expressing cells (Table 1).”
From Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function (2019) · cites this paper as [64]
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- Authors
- Zambelli, F., Pesole, G., & Pavesi, G.
- Affiliations
- University of Milan (IT)
- Corresponding author
- Pavesi, Giulio
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-31
- Volume
- 37
- Issue
- suppl_2
- Pages
- W247-W252
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2703934
- OpenAlex
- W2026731344
- Cited by
- 402
- References
- 2
- Citations by year
- 2026: 11 · 2025: 20 · 2024: 21 · 2023: 23 · 2022: 27 · 2021: 26 · 2020: 32 · 2019: 24 · 2018: 23 · 2017: 25 · 2016: 27 · 2015: 19 · 2014: 33 · 2013: 27 · 2012: 31
- FWCI
- 8.25
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, cc-by-nc)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- Ministero dell’Istruzione, dell’Università e della Ricerca
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- transcription factor binding sites, co-regulated genes, co-expressed genes, promoter, transcription factor binding specificity, gene expression regulation, DNA sequence analysis
- MeSH terms
- Binding Sites, Gene Expression Regulation, Promoter Regions, Genetic, Software, Transcription Factors, User-Computer Interface, Sequence Analysis, DNA
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