AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors
Abstract The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recen...
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| Veröffentlicht in: | Nucleic acids research 2019-01, Vol.47 (D1), p.D33-D38 |
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| container_title | Nucleic acids research |
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| creator | Hu, Hui Miao, Ya-Ru Jia, Long-Hao Yu, Qing-Yang Zhang, Qiong Guo, An-Yuan |
| description | Abstract
The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it. AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. These new features are: (i) more accurate TF family assignment rules; (ii) classification of transcription cofactors; (iii) TF binding sites information; (iv) the GWAS phenotype related information of human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (HumanTFDB) was designed for better utilizing the human TFs. The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation. |
| doi_str_mv | 10.1093/nar/gky822 |
| format | Article |
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The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it. AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. These new features are: (i) more accurate TF family assignment rules; (ii) classification of transcription cofactors; (iii) TF binding sites information; (iv) the GWAS phenotype related information of human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (HumanTFDB) was designed for better utilizing the human TFs. The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky822</identifier><identifier>PMID: 30204897</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Computational Biology - methods ; Database Issue ; Databases, Genetic ; Genome-Wide Association Study ; Humans ; Molecular Sequence Annotation ; Software ; Transcription Factors - metabolism ; User-Computer Interface ; Web Browser</subject><ispartof>Nucleic acids research, 2019-01, Vol.47 (D1), p.D33-D38</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0002-9208-1041</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/PMC6323978/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323978/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30204897$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hu, Hui</creatorcontrib><creatorcontrib>Miao, Ya-Ru</creatorcontrib><creatorcontrib>Jia, Long-Hao</creatorcontrib><creatorcontrib>Yu, Qing-Yang</creatorcontrib><creatorcontrib>Zhang, Qiong</creatorcontrib><creatorcontrib>Guo, An-Yuan</creatorcontrib><title>AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it. AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. These new features are: (i) more accurate TF family assignment rules; (ii) classification of transcription cofactors; (iii) TF binding sites information; (iv) the GWAS phenotype related information of human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (HumanTFDB) was designed for better utilizing the human TFs. The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.</description><subject>Animals</subject><subject>Computational Biology - methods</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>Genome-Wide Association Study</subject><subject>Humans</subject><subject>Molecular Sequence Annotation</subject><subject>Software</subject><subject>Transcription Factors - metabolism</subject><subject>User-Computer Interface</subject><subject>Web Browser</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNpVUcFOAjEQbYxGEL34AaYXjwttp3S7HkwARU1IvOC56Xa7sArtpruQ8PcWUKKnmXnvzctkHkK3lPQpyWDgdBgsvnaSsTPUpSBYwjPBzlGXABkmlHDZQVdN80kI5XTIL1EHCItolnZROXLVWq_m06cxhj55wBobv66DXVrXVFuLg238JhiLSx-wds63uq28i22Bo6yozGH0ZUT2TrgN2jUmVPUBL7VpfWiu0UWpV429-ak99DF9nk9ek9n7y9tkNEs8zaBNeGpynUoiJCelscwKyg1IAkVOgEtS5ABAraRcpAyYToe2MNoIsEJrWljoocejb73J15GzLp6zUnWIp4Wd8rpS_xlXLdXCb5UABlkqo8HdX4PT5u_HouD-KPCb-sRSovZJqJiEOiYB3zmBfHo</recordid><startdate>20190108</startdate><enddate>20190108</enddate><creator>Hu, Hui</creator><creator>Miao, Ya-Ru</creator><creator>Jia, Long-Hao</creator><creator>Yu, Qing-Yang</creator><creator>Zhang, Qiong</creator><creator>Guo, An-Yuan</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-9208-1041</orcidid></search><sort><creationdate>20190108</creationdate><title>AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors</title><author>Hu, Hui ; Miao, Ya-Ru ; Jia, Long-Hao ; Yu, Qing-Yang ; Zhang, Qiong ; Guo, An-Yuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-o193t-47cba7806840fce2e614c3803db03480db3331e81467232a75edcac63e6aa1de3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Animals</topic><topic>Computational Biology - methods</topic><topic>Database Issue</topic><topic>Databases, Genetic</topic><topic>Genome-Wide Association Study</topic><topic>Humans</topic><topic>Molecular Sequence Annotation</topic><topic>Software</topic><topic>Transcription Factors - metabolism</topic><topic>User-Computer Interface</topic><topic>Web Browser</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hu, Hui</creatorcontrib><creatorcontrib>Miao, Ya-Ru</creatorcontrib><creatorcontrib>Jia, Long-Hao</creatorcontrib><creatorcontrib>Yu, Qing-Yang</creatorcontrib><creatorcontrib>Zhang, Qiong</creatorcontrib><creatorcontrib>Guo, An-Yuan</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hu, Hui</au><au>Miao, Ya-Ru</au><au>Jia, Long-Hao</au><au>Yu, Qing-Yang</au><au>Zhang, Qiong</au><au>Guo, An-Yuan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2019-01-08</date><risdate>2019</risdate><volume>47</volume><issue>D1</issue><spage>D33</spage><epage>D38</epage><pages>D33-D38</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it. AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. These new features are: (i) more accurate TF family assignment rules; (ii) classification of transcription cofactors; (iii) TF binding sites information; (iv) the GWAS phenotype related information of human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (HumanTFDB) was designed for better utilizing the human TFs. The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>30204897</pmid><doi>10.1093/nar/gky822</doi><orcidid>https://orcid.org/0000-0002-9208-1041</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Computational Biology - methods Database Issue Databases, Genetic Genome-Wide Association Study Humans Molecular Sequence Annotation Software Transcription Factors - metabolism User-Computer Interface Web Browser |
| title | AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors |
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