Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
<p>Abstract</p> <p>Background</p> <p>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...
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| Format: | Article |
| Language: | English |
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BMC
2002-02-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/3/7 |
| _version_ | 1828737704290942976 |
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| author | Provero Paolo Cunto Ferdinando Di Caselle Michele |
| author_facet | Provero Paolo Cunto Ferdinando Di Caselle Michele |
| author_sort | Provero Paolo |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>The method was tested by applying it to the genome of <it>Saccharomyces cerevisiae</it>, 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.</p> <p>Conclusions</p> <p>We have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.</p> |
| first_indexed | 2024-04-12T23:49:37Z |
| format | Article |
| id | doaj.art-cfeaf8a80d9748fe8203eac2928889df |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T23:49:37Z |
| publishDate | 2002-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-cfeaf8a80d9748fe8203eac2928889df2022-12-22T03:11:46ZengBMCBMC Bioinformatics1471-21052002-02-0131710.1186/1471-2105-3-7Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotesProvero PaoloCunto Ferdinando DiCaselle Michele<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>The method was tested by applying it to the genome of <it>Saccharomyces cerevisiae</it>, 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.</p> <p>Conclusions</p> <p>We have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.</p>http://www.biomedcentral.com/1471-2105/3/7 |
| spellingShingle | Provero Paolo Cunto Ferdinando Di Caselle Michele Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes BMC Bioinformatics |
| title | Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes |
| title_full | Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes |
| title_fullStr | Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes |
| title_full_unstemmed | Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes |
| title_short | Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes |
| title_sort | correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes |
| url | http://www.biomedcentral.com/1471-2105/3/7 |
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