NucMap: a database of genome-wide nucleosome positioning map across species
Abstract Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. T...
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| Veröffentlicht in: | Nucleic acids research 2019-01, Vol.47 (D1), p.D163-D169 |
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| container_title | Nucleic acids research |
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| creator | Zhao, Yongbing Wang, Jinyue Liang, Fang Liu, Yanxia Wang, Qi Zhang, Hao Jiang, Meiye Zhang, Zhewen Zhao, Wenming Bao, Yiming Zhang, Zhang Wu, Jiayan Asmann, Yan W Li, Rujiao Xiao, Jingfa |
| description | Abstract
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation. |
| doi_str_mv | 10.1093/nar/gky980 |
| format | Article |
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Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky980</identifier><identifier>PMID: 30335176</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Chromatin Assembly and Disassembly ; Database Issue ; Databases, Genetic ; Genome-Wide Association Study - methods ; Nucleosomes - metabolism ; Software ; User-Computer Interface ; Web Browser</subject><ispartof>Nucleic acids research, 2019-01, Vol.47 (D1), p.D163-D169</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><citedby>FETCH-LOGICAL-c474t-ebbdd5c8ee5ed9b9e49b4135d2034346a9a618709d280da5d2e84cab851fd3d43</citedby><cites>FETCH-LOGICAL-c474t-ebbdd5c8ee5ed9b9e49b4135d2034346a9a618709d280da5d2e84cab851fd3d43</cites><orcidid>0000-0002-9917-7425</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/PMC6323900/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323900/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30335176$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhao, Yongbing</creatorcontrib><creatorcontrib>Wang, Jinyue</creatorcontrib><creatorcontrib>Liang, Fang</creatorcontrib><creatorcontrib>Liu, Yanxia</creatorcontrib><creatorcontrib>Wang, Qi</creatorcontrib><creatorcontrib>Zhang, Hao</creatorcontrib><creatorcontrib>Jiang, Meiye</creatorcontrib><creatorcontrib>Zhang, Zhewen</creatorcontrib><creatorcontrib>Zhao, Wenming</creatorcontrib><creatorcontrib>Bao, Yiming</creatorcontrib><creatorcontrib>Zhang, Zhang</creatorcontrib><creatorcontrib>Wu, Jiayan</creatorcontrib><creatorcontrib>Asmann, Yan W</creatorcontrib><creatorcontrib>Li, Rujiao</creatorcontrib><creatorcontrib>Xiao, Jingfa</creatorcontrib><title>NucMap: a database of genome-wide nucleosome positioning map across species</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.</description><subject>Chromatin Assembly and Disassembly</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>Genome-Wide Association Study - methods</subject><subject>Nucleosomes - metabolism</subject><subject>Software</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>eNp9kE1LxDAQhoMoun5c_AGSiyBC3aRJu4kHQcQv_LroOUyT2TXaNrVpFf-91V1FL57CZB7emXkI2ebsgDMtxjW049nzu1ZsiYy4yNNE6jxdJiMmWJZwJtUaWY_xiTEueSZXyZpgQmR8ko_I1W1vb6A5pEAddFBARBqmdIZ1qDB58w5p3dsSQxxq2oToOx9qX89oBQ0F24YYaWzQeoybZGUKZcStxbtBHs5O708ukuu788uT4-vEyonsEiwK5zKrEDN0utAodSG5yFzKhBQyBw05VxOmXaqYg-EflbRQqIxPnXBSbJCjeW7TFxU6i3XXQmma1lfQvpsA3vzt1P7RzMKryUUqNGNDwN4ioA0vPcbOVD5aLEuoMfTRpDxNM8UUVwO6P0e_Lm1x-jOGM_Np3wz2zdz-AO_8XuwH_dY9ALtzIPTNf0EfuByPmw</recordid><startdate>20190108</startdate><enddate>20190108</enddate><creator>Zhao, Yongbing</creator><creator>Wang, Jinyue</creator><creator>Liang, Fang</creator><creator>Liu, Yanxia</creator><creator>Wang, Qi</creator><creator>Zhang, Hao</creator><creator>Jiang, Meiye</creator><creator>Zhang, Zhewen</creator><creator>Zhao, Wenming</creator><creator>Bao, Yiming</creator><creator>Zhang, Zhang</creator><creator>Wu, Jiayan</creator><creator>Asmann, Yan W</creator><creator>Li, Rujiao</creator><creator>Xiao, Jingfa</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>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-9917-7425</orcidid></search><sort><creationdate>20190108</creationdate><title>NucMap: a database of genome-wide nucleosome positioning map across species</title><author>Zhao, Yongbing ; Wang, Jinyue ; Liang, Fang ; Liu, Yanxia ; Wang, Qi ; Zhang, Hao ; Jiang, Meiye ; Zhang, Zhewen ; Zhao, Wenming ; Bao, Yiming ; Zhang, Zhang ; Wu, Jiayan ; Asmann, Yan W ; Li, Rujiao ; Xiao, Jingfa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-ebbdd5c8ee5ed9b9e49b4135d2034346a9a618709d280da5d2e84cab851fd3d43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Chromatin Assembly and Disassembly</topic><topic>Database Issue</topic><topic>Databases, Genetic</topic><topic>Genome-Wide Association Study - methods</topic><topic>Nucleosomes - metabolism</topic><topic>Software</topic><topic>User-Computer Interface</topic><topic>Web Browser</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhao, Yongbing</creatorcontrib><creatorcontrib>Wang, Jinyue</creatorcontrib><creatorcontrib>Liang, Fang</creatorcontrib><creatorcontrib>Liu, Yanxia</creatorcontrib><creatorcontrib>Wang, Qi</creatorcontrib><creatorcontrib>Zhang, Hao</creatorcontrib><creatorcontrib>Jiang, Meiye</creatorcontrib><creatorcontrib>Zhang, Zhewen</creatorcontrib><creatorcontrib>Zhao, Wenming</creatorcontrib><creatorcontrib>Bao, Yiming</creatorcontrib><creatorcontrib>Zhang, Zhang</creatorcontrib><creatorcontrib>Wu, Jiayan</creatorcontrib><creatorcontrib>Asmann, Yan W</creatorcontrib><creatorcontrib>Li, Rujiao</creatorcontrib><creatorcontrib>Xiao, Jingfa</creatorcontrib><collection>Oxford Open</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><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>Zhao, Yongbing</au><au>Wang, Jinyue</au><au>Liang, Fang</au><au>Liu, Yanxia</au><au>Wang, Qi</au><au>Zhang, Hao</au><au>Jiang, Meiye</au><au>Zhang, Zhewen</au><au>Zhao, Wenming</au><au>Bao, Yiming</au><au>Zhang, Zhang</au><au>Wu, Jiayan</au><au>Asmann, Yan W</au><au>Li, Rujiao</au><au>Xiao, Jingfa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>NucMap: a database of genome-wide nucleosome positioning map across species</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>D163</spage><epage>D169</epage><pages>D163-D169</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>30335176</pmid><doi>10.1093/nar/gky980</doi><orcidid>https://orcid.org/0000-0002-9917-7425</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Full-Text Journals in Chemistry (Open access); DOAJ Directory of Open Access Journals; Oxford Open; PubMed Central |
| subjects | Chromatin Assembly and Disassembly Database Issue Databases, Genetic Genome-Wide Association Study - methods Nucleosomes - metabolism Software User-Computer Interface Web Browser |
| title | NucMap: a database of genome-wide nucleosome positioning map across species |
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