dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulatio...
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| Veröffentlicht in: | Database : the journal of biological databases and curation 2015, Vol.2015, p.bav052-bav052 |
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| container_title | Database : the journal of biological databases and curation |
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| creator | Choi, Jaeyoung Kim, Ki-Tae Huh, Aram Kwon, Seomun Hong, Changyoung Asiegbu, Fred O Jeon, Junhyun Lee, Yong-Hwan |
| description | Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. |
| doi_str_mv | 10.1093/database/bav052 |
| format | Article |
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Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies.</description><identifier>ISSN: 1758-0463</identifier><identifier>EISSN: 1758-0463</identifier><identifier>DOI: 10.1093/database/bav052</identifier><identifier>PMID: 26055100</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Acetylation ; Chromatin ; Databases, Protein ; Enzymes ; Epigenesis, Genetic ; Epigenetics ; Epigenomics - methods ; Gene expression ; Histones - genetics ; Histones - metabolism ; Methylation ; Original ; Protein Processing, Post-Translational ; Proteome - genetics ; Proteome - metabolism ; Web Browser</subject><ispartof>Database : the journal of biological databases and curation, 2015, Vol.2015, p.bav052-bav052</ispartof><rights>The Author(s) 2015. Published by Oxford University Press.</rights><rights>The Author(s) 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>The Author(s) 2015. Published by Oxford University Press. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c421t-3601de3ea672feb4e445b904afd3610d1c039e6c8fd545377d65cb28e243f4773</citedby><cites>FETCH-LOGICAL-c421t-3601de3ea672feb4e445b904afd3610d1c039e6c8fd545377d65cb28e243f4773</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460409/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460409/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,4024,27923,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26055100$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Choi, Jaeyoung</creatorcontrib><creatorcontrib>Kim, Ki-Tae</creatorcontrib><creatorcontrib>Huh, Aram</creatorcontrib><creatorcontrib>Kwon, Seomun</creatorcontrib><creatorcontrib>Hong, Changyoung</creatorcontrib><creatorcontrib>Asiegbu, Fred O</creatorcontrib><creatorcontrib>Jeon, Junhyun</creatorcontrib><creatorcontrib>Lee, Yong-Hwan</creatorcontrib><title>dbHiMo: a web-based epigenomics platform for histone-modifying enzymes</title><title>Database : the journal of biological databases and curation</title><addtitle>Database (Oxford)</addtitle><description>Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies.</description><subject>Acetylation</subject><subject>Chromatin</subject><subject>Databases, Protein</subject><subject>Enzymes</subject><subject>Epigenesis, Genetic</subject><subject>Epigenetics</subject><subject>Epigenomics - methods</subject><subject>Gene expression</subject><subject>Histones - genetics</subject><subject>Histones - metabolism</subject><subject>Methylation</subject><subject>Original</subject><subject>Protein Processing, Post-Translational</subject><subject>Proteome - genetics</subject><subject>Proteome - metabolism</subject><subject>Web Browser</subject><issn>1758-0463</issn><issn>1758-0463</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdUU1Lw0AQXUSxtXr2JgEvXmJ3s1-pB0GKtULFi56XTXbSbkmyMZtU6q83pR9ULzMD8-bx5j2Ergm-J3hEh0Y3OtEeholeYR6doD6RPA4xE_T0aO6hC--XGAsZx-wc9SKBOScY99HEJFP75h4CHXxDEm64TACVnUPpCpv6oMp1k7m6CLoSLKxvXAlh4YzN1racB1D-rAvwl-gs07mHq10foM_J88d4Gs7eX17HT7MwZRFpQiowMUBBCxllkDBgjCcjzHRmqCDYkBTTEYg0zgxnnEppBE-TKIaI0YxJSQfocctbtUkBJoWyqXWuqtoWul4rp636uyntQs3dSjEmMOscG6C7HUHtvlrwjSqsTyHPdQmu9YqIWFLGORUd9PYfdOnauuzeU52xnYMywhtFwy0qrZ33NWQHMQSrTUZqn5HaZtRd3Bz_cMDvQ6G_ONGQHg</recordid><startdate>2015</startdate><enddate>2015</enddate><creator>Choi, Jaeyoung</creator><creator>Kim, Ki-Tae</creator><creator>Huh, Aram</creator><creator>Kwon, Seomun</creator><creator>Hong, Changyoung</creator><creator>Asiegbu, Fred O</creator><creator>Jeon, Junhyun</creator><creator>Lee, Yong-Hwan</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>K9.</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>2015</creationdate><title>dbHiMo: a web-based epigenomics platform for histone-modifying enzymes</title><author>Choi, Jaeyoung ; Kim, Ki-Tae ; Huh, Aram ; Kwon, Seomun ; Hong, Changyoung ; Asiegbu, Fred O ; Jeon, Junhyun ; Lee, Yong-Hwan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c421t-3601de3ea672feb4e445b904afd3610d1c039e6c8fd545377d65cb28e243f4773</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Acetylation</topic><topic>Chromatin</topic><topic>Databases, Protein</topic><topic>Enzymes</topic><topic>Epigenesis, Genetic</topic><topic>Epigenetics</topic><topic>Epigenomics - methods</topic><topic>Gene expression</topic><topic>Histones - genetics</topic><topic>Histones - metabolism</topic><topic>Methylation</topic><topic>Original</topic><topic>Protein Processing, Post-Translational</topic><topic>Proteome - genetics</topic><topic>Proteome - metabolism</topic><topic>Web Browser</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Choi, Jaeyoung</creatorcontrib><creatorcontrib>Kim, Ki-Tae</creatorcontrib><creatorcontrib>Huh, Aram</creatorcontrib><creatorcontrib>Kwon, Seomun</creatorcontrib><creatorcontrib>Hong, Changyoung</creatorcontrib><creatorcontrib>Asiegbu, Fred O</creatorcontrib><creatorcontrib>Jeon, Junhyun</creatorcontrib><creatorcontrib>Lee, Yong-Hwan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Database : the journal of biological databases and curation</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Choi, Jaeyoung</au><au>Kim, Ki-Tae</au><au>Huh, Aram</au><au>Kwon, Seomun</au><au>Hong, Changyoung</au><au>Asiegbu, Fred O</au><au>Jeon, Junhyun</au><au>Lee, Yong-Hwan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>dbHiMo: a web-based epigenomics platform for histone-modifying enzymes</atitle><jtitle>Database : the journal of biological databases and curation</jtitle><addtitle>Database (Oxford)</addtitle><date>2015</date><risdate>2015</risdate><volume>2015</volume><spage>bav052</spage><epage>bav052</epage><pages>bav052-bav052</pages><issn>1758-0463</issn><eissn>1758-0463</eissn><abstract>Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>26055100</pmid><doi>10.1093/database/bav052</doi><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central |
| subjects | Acetylation Chromatin Databases, Protein Enzymes Epigenesis, Genetic Epigenetics Epigenomics - methods Gene expression Histones - genetics Histones - metabolism Methylation Original Protein Processing, Post-Translational Proteome - genetics Proteome - metabolism Web Browser |
| title | dbHiMo: a web-based epigenomics platform for histone-modifying enzymes |
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