dorsal/arxiv
View SchemaCorrelating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
| Authors | M. Caselle, F. Di Cunto, P. Provero |
|---|---|
| Categories | |
| ArXiv ID | physics/0203013 |
| URL | https://arxiv.org/abs/physics/0203013 |
| Journal | BMC Bioinformatics 2002, 3:7 |
Abstract
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.
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"abstract": "Gene regulation in eukaryotes is mainly effected through transcription\nfactors binding to rather short recognition motifs generally located upstream\nof the coding region. We present a novel computational method to identify\nregulatory elements in the upstream region of eukaryotic genes. The genes are\ngrouped in sets sharing an overrepresented short motif in their upstream\nsequence. For each set, the average expression level from a microarray\nexperiment is determined: If this level is significantly higher or lower than\nthe average taken over the whole genome, then the overerpresented motif shared\nby the genes in the set is likely to play a role in their regulation. The\nmethod was tested by applying it to the genome of Saccharomyces cerevisiae,\nusing the publicly available results of a DNA microarray experiment, in which\nexpression levels for virtually all the genes were measured during the diauxic\nshift from fermentation to respiration. Several known motifs were correctly\nidentified, and a new candidate regulatory sequence was determined.",
"arxiv_id": "physics/0203013",
"authors": [
"M. Caselle",
"F. Di Cunto",
"P. Provero"
],
"categories": [
"physics.bio-ph",
"cond-mat",
"q-bio.MN"
],
"journal_ref": "BMC Bioinformatics 2002, 3:7",
"title": "Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes",
"url": "https://arxiv.org/abs/physics/0203013"
},
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