Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology
Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functiona...
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| description | Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2 e - 16 ) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686 e - 14 ) in GeneRIFs and GOA shows our annotation resource is very reliable. |
| doi_str_mv | 10.1155/2016/4130861 |
| format | Article |
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In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2 e - 16 ) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686 e - 14 ) in GeneRIFs and GOA shows our annotation resource is very reliable.</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2016/4130861</identifier><identifier>PMID: 27635398</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Publishing Corporation</publisher><subject>Annotations ; Anopheles ; Chromosome Mapping - methods ; Data mining ; Databases, Genetic ; Disease ; Documentation - methods ; Gene Ontology ; Genes ; Genes - genetics ; Genetic aspects ; Genetic Markers - genetics ; Genetic Predisposition to Disease - classification ; Genetic Predisposition to Disease - genetics ; Genome, Human - genetics ; Genomes ; Genomics ; Genotype & phenotype ; Humans ; Medical Subject Headings-MeSH ; MicroRNA ; MicroRNAs ; Ontology ; Polymorphism, Single Nucleotide - genetics ; Proteins</subject><ispartof>BioMed research international, 2016-01, Vol.2016 (2016), p.1-8</ispartof><rights>Copyright © 2016 Yang Hu et al.</rights><rights>COPYRIGHT 2016 John Wiley & Sons, Inc.</rights><rights>Copyright © 2016 Yang Hu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2016 Yang Hu et al. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c532t-15f63dc8565eea84f53b5c681326679473f8bf71ca6997c9a5e39c596fedd9e23</citedby><cites>FETCH-LOGICAL-c532t-15f63dc8565eea84f53b5c681326679473f8bf71ca6997c9a5e39c596fedd9e23</cites><orcidid>0000-0002-2318-432X ; 0000-0002-6665-6710 ; 0000-0001-6500-6217</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011202/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011202/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27635398$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Chen, Xing</contributor><creatorcontrib>Cheng, Liang</creatorcontrib><creatorcontrib>Wang, Yadong</creatorcontrib><creatorcontrib>Dong, Lixiang</creatorcontrib><creatorcontrib>Ren, Jun</creatorcontrib><creatorcontrib>Zhou, Wenyang</creatorcontrib><creatorcontrib>Hu, Yang</creatorcontrib><creatorcontrib>Jin, Shuilin</creatorcontrib><title>Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology</title><title>BioMed research international</title><addtitle>Biomed Res Int</addtitle><description>Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2 e - 16 ) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686 e - 14 ) in GeneRIFs and GOA shows our annotation resource is very reliable.</description><subject>Annotations</subject><subject>Anopheles</subject><subject>Chromosome Mapping - methods</subject><subject>Data mining</subject><subject>Databases, Genetic</subject><subject>Disease</subject><subject>Documentation - methods</subject><subject>Gene Ontology</subject><subject>Genes</subject><subject>Genes - genetics</subject><subject>Genetic aspects</subject><subject>Genetic Markers - genetics</subject><subject>Genetic Predisposition to Disease - classification</subject><subject>Genetic Predisposition to Disease - genetics</subject><subject>Genome, Human - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Humans</subject><subject>Medical Subject Headings-MeSH</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>Ontology</subject><subject>Polymorphism, Single Nucleotide - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BioMed research international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cheng, Liang</au><au>Wang, Yadong</au><au>Dong, Lixiang</au><au>Ren, Jun</au><au>Zhou, Wenyang</au><au>Hu, Yang</au><au>Jin, Shuilin</au><au>Chen, Xing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology</atitle><jtitle>BioMed research international</jtitle><addtitle>Biomed Res Int</addtitle><date>2016-01-01</date><risdate>2016</risdate><volume>2016</volume><issue>2016</issue><spage>1</spage><epage>8</epage><pages>1-8</pages><issn>2314-6133</issn><eissn>2314-6141</eissn><abstract>Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2 e - 16 ) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686 e - 14 ) in GeneRIFs and GOA shows our annotation resource is very reliable.</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Publishing Corporation</pub><pmid>27635398</pmid><doi>10.1155/2016/4130861</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-2318-432X</orcidid><orcidid>https://orcid.org/0000-0002-6665-6710</orcidid><orcidid>https://orcid.org/0000-0001-6500-6217</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Annotations Anopheles Chromosome Mapping - methods Data mining Databases, Genetic Disease Documentation - methods Gene Ontology Genes Genes - genetics Genetic aspects Genetic Markers - genetics Genetic Predisposition to Disease - classification Genetic Predisposition to Disease - genetics Genome, Human - genetics Genomes Genomics Genotype & phenotype Humans Medical Subject Headings-MeSH MicroRNA MicroRNAs Ontology Polymorphism, Single Nucleotide - genetics Proteins |
| title | Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology |
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