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Integrating regulatory motif discovery and genome-wide expression analysis
Open accessAbstract
We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. motif regressor is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions. When applied to Saccharomyces cerevisiae , motif regressor identified the ROX1 and YAP1 motifs from Rox1p and Yap1p overexpression experiments, respectively; predicted that Gcn4p may have increased activity in YAP1 deletion mutants; reported a group of motifs (including GCN4, PHO4, MET4, STRE, USR1, RAP1, M3A, and M3B) that may mediate the transcriptional response to amino acid starvation; and found all of the known cell-cycle regulation motifs from 18 expression microarrays over two cell cycles.
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“A similar linear regression-based model was previously proposed to predict transcription factor regulatory activities and motifs from yeast gene expression data56.”
From Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease (2023) · cites this paper as [56]
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Metadata
- Authors
- Conlon, E. M., Liu, X. S., Lieb, J. D., & Liu, J. S.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Liu, X. Shirley
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2003-03-07
- Volume
- 100
- Issue
- 6
- Pages
- 3339-3344
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC152294
- OpenAlex
- W2096139934
- Cited by
- 343
- References
- 32
- Citations by year
- 2026: 1 · 2025: 2 · 2023: 6 · 2022: 2 · 2021: 2 · 2020: 7 · 2019: 8 · 2018: 5 · 2017: 2 · 2016: 11 · 2015: 9 · 2014: 6 · 2013: 11 · 2012: 21
- FWCI
- 12.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- UNC Libraries
- Funders
- National Science Foundation (0204674)
- Helen Hay Whitney Foundation
- National Institutes of Health
- National Human Genome Research Institute (R01HG002518, R01-HG02518-01)
- U.S. National Library of Medicine (1F37 LM 07626-01, F37LM007626)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- regulatory motif discovery, upstream promoter sequences, gene expression changes, transcription factor binding sites, Saccharomyces cerevisiae, Gcn4p, cell cycle regulation, transcriptional regulation
- MeSH terms
- Algorithms, Base Sequence, Cell Cycle, DNA, Fungal, Genes, Fungal, Genes, Regulator, Saccharomyces cerevisiae, Linear Models, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Genomics
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