Computational analysis of microRNA function in heart development
Emerging evidence suggests that specific spatio-temporal microRNA （miRNA） expression is required for heart development. In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order t...
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| Veröffentlicht in: | Acta biochimica et biophysica Sinica 2010-09, Vol.42 (9), p.662-670 |
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| container_title | Acta biochimica et biophysica Sinica |
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| creator | Liu, Ganqiang Ding, Min Chen, Jiajia Huang, Jinyan Wang, Haiyun Jing, Qing Shen, Bairong |
| description | Emerging evidence suggests that specific spatio-temporal microRNA （miRNA） expression is required for heart development. In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order to provide a global perspective for the biologists who study the relationship between differentially expressed miRNAs and heart development, we employed computational analysis to uncover the specific cellular processes and biological pathways targeted by miRNAs in mouse heart development. Here, we utilized Gene Ontology （GO） categories, KEGG Pathway, and GeneGo Pathway Maps as a gene functional annotation system for miRNA target enrichment analysis. The target genes of miRNAs were found to be enriched in functional categories and pathway maps in which miRNAs could play important roles during heart development. Meanwhile, we developed miRHrt （http：//sysbio.suda.edu. cn/mirhrt/）, a database aiming to provide a comprehensive resource of miRNA function in regulating heart development. These computational analysis results effectively illustrated the correlation of differentially expressed miRNAs with cellular functions and heart development. We hope that the identified novel heart development- associated pathways and the database presented here would facilitate further understanding of the roles and mechanisms of miRNAs in heart development. |
| doi_str_mv | 10.1093/abbs/gmq072 |
| format | Article |
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In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order to provide a global perspective for the biologists who study the relationship between differentially expressed miRNAs and heart development, we employed computational analysis to uncover the specific cellular processes and biological pathways targeted by miRNAs in mouse heart development. Here, we utilized Gene Ontology （GO） categories, KEGG Pathway, and GeneGo Pathway Maps as a gene functional annotation system for miRNA target enrichment analysis. The target genes of miRNAs were found to be enriched in functional categories and pathway maps in which miRNAs could play important roles during heart development. Meanwhile, we developed miRHrt （http：//sysbio.suda.edu. cn/mirhrt/）, a database aiming to provide a comprehensive resource of miRNA function in regulating heart development. These computational analysis results effectively illustrated the correlation of differentially expressed miRNAs with cellular functions and heart development. We hope that the identified novel heart development- associated pathways and the database presented here would facilitate further understanding of the roles and mechanisms of miRNAs in heart development.</description><identifier>ISSN: 1672-9145</identifier><identifier>EISSN: 1745-7270</identifier><identifier>DOI: 10.1093/abbs/gmq072</identifier><identifier>PMID: 20716610</identifier><language>eng</language><publisher>China: Oxford University Press</publisher><subject>Algorithms ; Animals ; Computational Biology - methods ; Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Heart - embryology ; Heart - growth & development ; Internet ; Mice ; microRNA ; MicroRNAs - genetics ; MicroRNAs - metabolism ; MicroRNAs - physiology ; miRNA ; Myocardium - metabolism ; Signal Transduction ; 功能注释 ; 差异表达 ; 心脏发育 ; 生物学家 ; 靶基因</subject><ispartof>Acta biochimica et biophysica Sinica, 2010-09, Vol.42 (9), p.662-670</ispartof><rights>The Author 2010. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c383t-8b6a96390bd5f72c9456fcce8fdd4c268c27ab55f11f7ea6ddd041c336147dcb3</citedby><cites>FETCH-LOGICAL-c383t-8b6a96390bd5f72c9456fcce8fdd4c268c27ab55f11f7ea6ddd041c336147dcb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/90160X/90160X.jpg</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20716610$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Ganqiang</creatorcontrib><creatorcontrib>Ding, Min</creatorcontrib><creatorcontrib>Chen, Jiajia</creatorcontrib><creatorcontrib>Huang, Jinyan</creatorcontrib><creatorcontrib>Wang, Haiyun</creatorcontrib><creatorcontrib>Jing, Qing</creatorcontrib><creatorcontrib>Shen, Bairong</creatorcontrib><title>Computational analysis of microRNA function in heart development</title><title>Acta biochimica et biophysica Sinica</title><addtitle>Acta Biochimica et Biophysica Sinica</addtitle><description>Emerging evidence suggests that specific spatio-temporal microRNA （miRNA） expression is required for heart development. In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order to provide a global perspective for the biologists who study the relationship between differentially expressed miRNAs and heart development, we employed computational analysis to uncover the specific cellular processes and biological pathways targeted by miRNAs in mouse heart development. Here, we utilized Gene Ontology （GO） categories, KEGG Pathway, and GeneGo Pathway Maps as a gene functional annotation system for miRNA target enrichment analysis. The target genes of miRNAs were found to be enriched in functional categories and pathway maps in which miRNAs could play important roles during heart development. Meanwhile, we developed miRHrt （http：//sysbio.suda.edu. cn/mirhrt/）, a database aiming to provide a comprehensive resource of miRNA function in regulating heart development. These computational analysis results effectively illustrated the correlation of differentially expressed miRNAs with cellular functions and heart development. We hope that the identified novel heart development- associated pathways and the database presented here would facilitate further understanding of the roles and mechanisms of miRNAs in heart development.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Computational Biology - methods</subject><subject>Databases, Genetic</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Heart - embryology</subject><subject>Heart - growth & development</subject><subject>Internet</subject><subject>Mice</subject><subject>microRNA</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>MicroRNAs - physiology</subject><subject>miRNA</subject><subject>Myocardium - metabolism</subject><subject>Signal Transduction</subject><subject>功能注释</subject><subject>差异表达</subject><subject>心脏发育</subject><subject>生物学家</subject><subject>靶基因</subject><issn>1672-9145</issn><issn>1745-7270</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkM1LxDAQxYMo7rp68i7Fgx6kbtI0SXtzWfyCRUH0HPK5G22bbtMK-9_b0tWrh5l5MD_eDA-AcwRvEczxXEgZ5utyC1lyAKaIpSRmCYOHvaYsiXOUkgk4CeETQkwpgsdgkkCGBjkFd0tf1l0rWucrUUSib7vgQuRtVDrV-LeXRWS7Sg37yFXRxoimjbT5NoWvS1O1p-DIiiKYs_2cgY-H-_flU7x6fXxeLlaxwhlu40xSkVOcQ6mJZYnKU0KtUiazWqcqoZlKmJCEWIQsM4JqrWGKFMYUpUwriWfgevStG7_tTGh56YIyRSEq47vAWZrlfUHUkzcj2b8fQmMsrxtXimbHEeRDYnxIjI-J9fTF3reTpdF_7G9EPXA1Ar6r_3G63N_d-Gq9ddWaS6G-rCsMx4TkhGUE_wAR-4D3</recordid><startdate>20100901</startdate><enddate>20100901</enddate><creator>Liu, Ganqiang</creator><creator>Ding, Min</creator><creator>Chen, Jiajia</creator><creator>Huang, Jinyan</creator><creator>Wang, Haiyun</creator><creator>Jing, Qing</creator><creator>Shen, Bairong</creator><general>Oxford University Press</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W94</scope><scope>WU4</scope><scope>~WA</scope><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>7X8</scope></search><sort><creationdate>20100901</creationdate><title>Computational analysis of microRNA function in heart development</title><author>Liu, Ganqiang ; Ding, Min ; Chen, Jiajia ; Huang, Jinyan ; Wang, Haiyun ; Jing, Qing ; Shen, Bairong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c383t-8b6a96390bd5f72c9456fcce8fdd4c268c27ab55f11f7ea6ddd041c336147dcb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Computational Biology - methods</topic><topic>Databases, Genetic</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Heart - embryology</topic><topic>Heart - growth & development</topic><topic>Internet</topic><topic>Mice</topic><topic>microRNA</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>MicroRNAs - physiology</topic><topic>miRNA</topic><topic>Myocardium - metabolism</topic><topic>Signal Transduction</topic><topic>功能注释</topic><topic>差异表达</topic><topic>心脏发育</topic><topic>生物学家</topic><topic>靶基因</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Ganqiang</creatorcontrib><creatorcontrib>Ding, Min</creatorcontrib><creatorcontrib>Chen, Jiajia</creatorcontrib><creatorcontrib>Huang, Jinyan</creatorcontrib><creatorcontrib>Wang, Haiyun</creatorcontrib><creatorcontrib>Jing, Qing</creatorcontrib><creatorcontrib>Shen, Bairong</creatorcontrib><collection>中文科技期刊数据库</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>中文科技期刊数据库-7.0平台</collection><collection>中文科技期刊数据库-自然科学</collection><collection>中文科技期刊数据库-自然科学-生物科学</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Acta biochimica et biophysica Sinica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Ganqiang</au><au>Ding, Min</au><au>Chen, Jiajia</au><au>Huang, Jinyan</au><au>Wang, Haiyun</au><au>Jing, Qing</au><au>Shen, Bairong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Computational analysis of microRNA function in heart development</atitle><jtitle>Acta biochimica et biophysica Sinica</jtitle><addtitle>Acta Biochimica et Biophysica Sinica</addtitle><date>2010-09-01</date><risdate>2010</risdate><volume>42</volume><issue>9</issue><spage>662</spage><epage>670</epage><pages>662-670</pages><issn>1672-9145</issn><eissn>1745-7270</eissn><abstract>Emerging evidence suggests that specific spatio-temporal microRNA （miRNA） expression is required for heart development. In recent years, hundreds of miRNAs have been discovered. In contrast, functional annotations are available only for a very small fraction of these regulatory molecules. In order to provide a global perspective for the biologists who study the relationship between differentially expressed miRNAs and heart development, we employed computational analysis to uncover the specific cellular processes and biological pathways targeted by miRNAs in mouse heart development. Here, we utilized Gene Ontology （GO） categories, KEGG Pathway, and GeneGo Pathway Maps as a gene functional annotation system for miRNA target enrichment analysis. The target genes of miRNAs were found to be enriched in functional categories and pathway maps in which miRNAs could play important roles during heart development. Meanwhile, we developed miRHrt （http：//sysbio.suda.edu. cn/mirhrt/）, a database aiming to provide a comprehensive resource of miRNA function in regulating heart development. 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| subjects | Algorithms Animals Computational Biology - methods Databases, Genetic Gene Expression Profiling Gene Expression Regulation, Developmental Heart - embryology Heart - growth & development Internet Mice microRNA MicroRNAs - genetics MicroRNAs - metabolism MicroRNAs - physiology miRNA Myocardium - metabolism Signal Transduction 功能注释 差异表达 心脏发育 生物学家 靶基因 |
| title | Computational analysis of microRNA function in heart development |
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