PASTAA: identifying transcription factors associated with sets of co-regulated genes
Open accessAbstract
Motivation: A major challenge in regulatory genomics is the identification of associations between functional categories of genes (e.g. tissues, metabolic pathways) and their regulating transcription factors (TFs). While, for a limited number of categories, the regulating TFs are already known, still for many functional categories the responsible factors remain to be elucidated. Results: We put forward a novel method (PASTAA) for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a TF to promoters. This binding strength information is compared to the likelihood of membership of the corresponding genes in the functional category under study. Coherence between the two ranked datasets is seen as an indicator of association between a TF and the category. PASTAA is applied primarily to the determination of TFs driving tissue-specific expression. We show that PASTAA is capable of recovering many TFs acting tissue specifically and, in addition, provides novel associations so far not detected by alternative methods. The application of PASTAA to detect TFs involved in the regulation of tissue-specific gene expression revealed a remarkable number of experimentally supported associations. The validated success for various datasets implies that PASTAA can directly be applied for the detection of TFs associated with newly derived gene sets. Availability: The PASTAA source code as well as a corresponding web interface is freely available at http://trap.molgen.mpg.de Contact: roider@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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 [63]
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- Authors
- Roider, H. G., Manke, T., O'Keeffe, S., Vingron, M., & Haas, S. A.
- Affiliations
- Max Planck Society (DE)
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin
- Max Planck Institute for Molecular Genetics (DE)
- Corresponding author
- Roider, Helge G.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-12-09
- Volume
- 25
- Issue
- 4
- Pages
- 435-442
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2642637
- OpenAlex
- W2133045519
- Cited by
- 154
- References
- 2
- Citations by year
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- FWCI
- 3.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Max Planck Institute for Plasma Physics (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- transcription factors, co-regulated genes, functional categories, tissue-specific gene expression, promoter binding, regulatory genomics
- MeSH terms
- Binding Sites, Gene Expression Regulation, Promoter Regions, Genetic, Software, Transcription Factors, Expressed Sequence Tags, Gene Expression Profiling, Databases, Genetic, Chromatin Immunoprecipitation
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