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A framework for exploring functional variability in olfactory receptor genes
Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, O...
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| Published in: | PloS one 2007-08, Vol.2 (8), p.e682-e682 |
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| creator | Man, Orna Willhite, David C Crasto, Chiquito J Shepherd, Gordon M Gilad, Yoav |
| description | Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested.
Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region.
Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability. |
| doi_str_mv | 10.1371/journal.pone.0000682 |
| format | article |
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Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region.
Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0000682</identifier><identifier>PMID: 17668060</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Amino Acid Sequence ; Amino acids ; Analogies ; Analysis ; Animal genetics ; Animals ; Binding ; Binding sites ; Chemical Biology ; Classification ; Cluster Analysis ; Coding ; Enzymes ; Genes ; Genetic Variation ; Genetics and Genomics/Bioinformatics ; Genomes ; Genomics ; Humans ; Kinases ; Ligands ; Mice ; Molecular Sequence Data ; Mutation ; Neural coding ; Neurobiology ; Neurosciences ; Odorant receptors ; Odorants ; Olfactory Receptor Neurons - physiology ; Orphan receptors ; Pentanoic Acids - chemistry ; Phylogeny ; Proteins ; Receptors ; Receptors, Odorant - classification ; Receptors, Odorant - genetics ; Sequence Alignment ; Transcription factors ; Variability</subject><ispartof>PloS one, 2007-08, Vol.2 (8), p.e682-e682</ispartof><rights>COPYRIGHT 2007 Public Library of Science</rights><rights>2007 Man et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Man et al. 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c592t-b05aab99fb1f358a4d19bca9dd5690a07a4a4f43704a0aefaaf23998ea71d73</citedby><cites>FETCH-LOGICAL-c592t-b05aab99fb1f358a4d19bca9dd5690a07a4a4f43704a0aefaaf23998ea71d73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1289159506/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1289159506?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17668060$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Baxter, Ivan</contributor><creatorcontrib>Man, Orna</creatorcontrib><creatorcontrib>Willhite, David C</creatorcontrib><creatorcontrib>Crasto, Chiquito J</creatorcontrib><creatorcontrib>Shepherd, Gordon M</creatorcontrib><creatorcontrib>Gilad, Yoav</creatorcontrib><title>A framework for exploring functional variability in olfactory receptor genes</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested.
Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region.
Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analogies</subject><subject>Analysis</subject><subject>Animal genetics</subject><subject>Animals</subject><subject>Binding</subject><subject>Binding sites</subject><subject>Chemical Biology</subject><subject>Classification</subject><subject>Cluster Analysis</subject><subject>Coding</subject><subject>Enzymes</subject><subject>Genes</subject><subject>Genetic Variation</subject><subject>Genetics and Genomics/Bioinformatics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Kinases</subject><subject>Ligands</subject><subject>Mice</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Neural coding</subject><subject>Neurobiology</subject><subject>Neurosciences</subject><subject>Odorant receptors</subject><subject>Odorants</subject><subject>Olfactory Receptor Neurons - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Man, Orna</au><au>Willhite, David C</au><au>Crasto, Chiquito J</au><au>Shepherd, Gordon M</au><au>Gilad, Yoav</au><au>Baxter, Ivan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A framework for exploring functional variability in olfactory receptor genes</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2007-08-01</date><risdate>2007</risdate><volume>2</volume><issue>8</issue><spage>e682</spage><epage>e682</epage><pages>e682-e682</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested.
Here, we propose an alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach is based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region.
Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regions. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>17668060</pmid><doi>10.1371/journal.pone.0000682</doi><tpages>e682</tpages><oa>free_for_read</oa></addata></record> |
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| language | eng |
| recordid | cdi_plos_journals_1289159506 |
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| subjects | Algorithms Amino Acid Sequence Amino acids Analogies Analysis Animal genetics Animals Binding Binding sites Chemical Biology Classification Cluster Analysis Coding Enzymes Genes Genetic Variation Genetics and Genomics/Bioinformatics Genomes Genomics Humans Kinases Ligands Mice Molecular Sequence Data Mutation Neural coding Neurobiology Neurosciences Odorant receptors Odorants Olfactory Receptor Neurons - physiology Orphan receptors Pentanoic Acids - chemistry Phylogeny Proteins Receptors Receptors, Odorant - classification Receptors, Odorant - genetics Sequence Alignment Transcription factors Variability |
| title | A framework for exploring functional variability in olfactory receptor genes |
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