Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
<p>Abstract</p> <p>Background</p> <p>3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2007-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/174 |
| _version_ | 1811249676469403648 |
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| author | Caselle Michele Di Cunto Ferdinando Corà Davide Provero Paolo |
| author_facet | Caselle Michele Di Cunto Ferdinando Corà Davide Provero Paolo |
| author_sort | Caselle Michele |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years.</p> <p>Results</p> <p>We propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs.</p> <p>Conclusion</p> <p>Both methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification.</p> |
| first_indexed | 2024-04-12T15:51:46Z |
| format | Article |
| id | doaj.art-6ea33a73f0304c75af5af780f74741e9 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T15:51:46Z |
| publishDate | 2007-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-6ea33a73f0304c75af5af780f74741e92022-12-22T03:26:29ZengBMCBMC Bioinformatics1471-21052007-05-018117410.1186/1471-2105-8-174Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributionsCaselle MicheleDi Cunto FerdinandoCorà DavideProvero Paolo<p>Abstract</p> <p>Background</p> <p>3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years.</p> <p>Results</p> <p>We propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs.</p> <p>Conclusion</p> <p>Both methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification.</p>http://www.biomedcentral.com/1471-2105/8/174 |
| spellingShingle | Caselle Michele Di Cunto Ferdinando Corà Davide Provero Paolo Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions BMC Bioinformatics |
| title | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions |
| title_full | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions |
| title_fullStr | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions |
| title_full_unstemmed | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions |
| title_short | Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions |
| title_sort | identification of candidate regulatory sequences in mammalian 3 utrs by statistical analysis of oligonucleotide distributions |
| url | http://www.biomedcentral.com/1471-2105/8/174 |
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