ArticleBMC genomics2004
Combined analysis of expression data and transcription factor binding sites in the yeast genome.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Article
- Tight Regulation of Srs2 Helicase Activity Is Crucial for Proper Functioning of DNA Repair Mechanisms.G3 (Bethesda, Md.) · 2018Article
- Regulated antisense transcription controls expression of cell-type-specific genes in yeast.Molecular and cellular biology · 2011Article
- Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia.Genome biology · 2008Article
- Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression.BMC genomics · 2006Article
- Three-pronged genomic analysis reveals yeast cell-type regulation circuitry.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Repression of the yeast HO gene by the MATalpha2 and MATa1 homeodomain proteins.Nucleic acids research · 2004Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe analysis of gene expression using DNA microarrays provides genome wide profiles of the genes controlled by the presence or absence of a specific transcription factor. However, the question arises of whether a change in the level of transcription of a specific gene is caused by the transcription factor acting directly at the promoter of the gene or through regulation of other transcription factors working at the promoter.
resultsTo address this problem we have devised a computational method that combines microarray expression and site preference data. We have tested this approach by identifying functional targets of the a1-alpha2 complex, which represses haploid-specific genes in the yeast Saccharomyces cerevisiae. Our analysis identified many known or suspected haploid-specific genes that are direct targets of the a1-alpha2 complex, as well as a number of previously uncharacterized targets. We were also able to identify a number of haploid-specific genes which do not appear to be direct targets of the a1-alpha2 complex, as well as a1-alpha2 target sites that do not repress transcription of nearby genes. Our method has a much lower false positive rate when compared to some of the conventional bioinformatic approaches.
conclusionsThese findings show advantages of combining these two forms of data to investigate the mechanism of co-regulation of specific sets of genes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.