SEanalysis: a web tool for super-enhancer associated regulatory analysis
Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analy...
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| Veröffentlicht in: | Nucleic acids research 2019-07, Vol.47 (W1), p.W248-W255 |
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| creator | Qian, Feng-Cui Li, Xue-Cang Guo, Jin-Cheng Zhao, Jian-Mei Li, Yan-Yu Tang, Zhi-Dong Zhou, Li-Wei Zhang, Jian Bai, Xue-Feng Jiang, Yong Pan, Qi Wang, Qiu-Yu Li, En-Min Li, Chun-Quan Xu, Li-Yan Lin, De-Chen |
| description | Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis. |
| doi_str_mv | 10.1093/nar/gkz302 |
| format | Article |
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To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkz302</identifier><identifier>PMID: 31028388</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Binding Sites - genetics ; Databases, Genetic ; Enhancer Elements, Genetic - genetics ; Gene Expression Regulation - genetics ; Gene Regulatory Networks - genetics ; Humans ; Internet ; Software ; Transcription Factors - genetics ; Web Server Issue</subject><ispartof>Nucleic acids research, 2019-07, Vol.47 (W1), p.W248-W255</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2019. 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-c444t-3229b77c5d9cd0b543ff8d2b8d7975f8438a3092bde720916c9eeb0a74da8e4e3</citedby><cites>FETCH-LOGICAL-c444t-3229b77c5d9cd0b543ff8d2b8d7975f8438a3092bde720916c9eeb0a74da8e4e3</cites><orcidid>0000-0002-1618-4292</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/PMC6602466/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602466/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31028388$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Qian, Feng-Cui</creatorcontrib><creatorcontrib>Li, Xue-Cang</creatorcontrib><creatorcontrib>Guo, Jin-Cheng</creatorcontrib><creatorcontrib>Zhao, Jian-Mei</creatorcontrib><creatorcontrib>Li, Yan-Yu</creatorcontrib><creatorcontrib>Tang, Zhi-Dong</creatorcontrib><creatorcontrib>Zhou, Li-Wei</creatorcontrib><creatorcontrib>Zhang, Jian</creatorcontrib><creatorcontrib>Bai, Xue-Feng</creatorcontrib><creatorcontrib>Jiang, Yong</creatorcontrib><creatorcontrib>Pan, Qi</creatorcontrib><creatorcontrib>Wang, Qiu-Yu</creatorcontrib><creatorcontrib>Li, En-Min</creatorcontrib><creatorcontrib>Li, Chun-Quan</creatorcontrib><creatorcontrib>Xu, Li-Yan</creatorcontrib><creatorcontrib>Lin, De-Chen</creatorcontrib><title>SEanalysis: a web tool for super-enhancer associated regulatory analysis</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.</description><subject>Binding Sites - genetics</subject><subject>Databases, Genetic</subject><subject>Enhancer Elements, Genetic - genetics</subject><subject>Gene Expression Regulation - genetics</subject><subject>Gene Regulatory Networks - genetics</subject><subject>Humans</subject><subject>Internet</subject><subject>Software</subject><subject>Transcription Factors - genetics</subject><subject>Web Server Issue</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkE1Lw0AQhhdRbK1e_AGyRxFi9yubXQ-ClGqFggf1vGw2kzaaZutuotRfb6RV9DSHed53hgehU0ouKdF83NgwXrx-csL20JByyRKhJdtHQ8JJmlAi1AAdxfhCCBU0FYdowClhiis1RLPHqW1svYlVvMIWf0COW-9rXPqAY7eGkECztI2DgG2M3lW2hQIHWHS1bX3Y4J_0MToobR3hZDdH6Pl2-jSZJfOHu_vJzTxxQog24YzpPMtcWmhXkDwVvCxVwXJVZDpLSyW4spxolheQMaKpdBogJzYThVUggI_Q9bZ33eUrKBw0bbC1WYdqZcPGeFuZ_5umWpqFfzdSEiak7AvOdwXBv3UQW7OqooO6tg34LhrGqOzlSKp79GKLuuBjDFD-nqHEfKs3vXqzVd_DZ38f-0V_XPMvpg2CDg</recordid><startdate>20190702</startdate><enddate>20190702</enddate><creator>Qian, Feng-Cui</creator><creator>Li, Xue-Cang</creator><creator>Guo, Jin-Cheng</creator><creator>Zhao, Jian-Mei</creator><creator>Li, Yan-Yu</creator><creator>Tang, Zhi-Dong</creator><creator>Zhou, Li-Wei</creator><creator>Zhang, Jian</creator><creator>Bai, Xue-Feng</creator><creator>Jiang, Yong</creator><creator>Pan, Qi</creator><creator>Wang, Qiu-Yu</creator><creator>Li, En-Min</creator><creator>Li, Chun-Quan</creator><creator>Xu, Li-Yan</creator><creator>Lin, De-Chen</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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-1618-4292</orcidid></search><sort><creationdate>20190702</creationdate><title>SEanalysis: a web tool for super-enhancer associated regulatory analysis</title><author>Qian, Feng-Cui ; Li, Xue-Cang ; Guo, Jin-Cheng ; Zhao, Jian-Mei ; Li, Yan-Yu ; Tang, Zhi-Dong ; Zhou, Li-Wei ; Zhang, Jian ; Bai, Xue-Feng ; Jiang, Yong ; Pan, Qi ; Wang, Qiu-Yu ; Li, En-Min ; Li, Chun-Quan ; Xu, Li-Yan ; Lin, De-Chen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c444t-3229b77c5d9cd0b543ff8d2b8d7975f8438a3092bde720916c9eeb0a74da8e4e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Binding Sites - genetics</topic><topic>Databases, Genetic</topic><topic>Enhancer Elements, Genetic - genetics</topic><topic>Gene Expression Regulation - genetics</topic><topic>Gene Regulatory Networks - genetics</topic><topic>Humans</topic><topic>Internet</topic><topic>Software</topic><topic>Transcription Factors - genetics</topic><topic>Web Server Issue</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Qian, Feng-Cui</creatorcontrib><creatorcontrib>Li, Xue-Cang</creatorcontrib><creatorcontrib>Guo, Jin-Cheng</creatorcontrib><creatorcontrib>Zhao, Jian-Mei</creatorcontrib><creatorcontrib>Li, Yan-Yu</creatorcontrib><creatorcontrib>Tang, Zhi-Dong</creatorcontrib><creatorcontrib>Zhou, Li-Wei</creatorcontrib><creatorcontrib>Zhang, Jian</creatorcontrib><creatorcontrib>Bai, Xue-Feng</creatorcontrib><creatorcontrib>Jiang, Yong</creatorcontrib><creatorcontrib>Pan, Qi</creatorcontrib><creatorcontrib>Wang, Qiu-Yu</creatorcontrib><creatorcontrib>Li, En-Min</creatorcontrib><creatorcontrib>Li, Chun-Quan</creatorcontrib><creatorcontrib>Xu, Li-Yan</creatorcontrib><creatorcontrib>Lin, De-Chen</creatorcontrib><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>Qian, Feng-Cui</au><au>Li, Xue-Cang</au><au>Guo, Jin-Cheng</au><au>Zhao, Jian-Mei</au><au>Li, Yan-Yu</au><au>Tang, Zhi-Dong</au><au>Zhou, Li-Wei</au><au>Zhang, Jian</au><au>Bai, Xue-Feng</au><au>Jiang, Yong</au><au>Pan, Qi</au><au>Wang, Qiu-Yu</au><au>Li, En-Min</au><au>Li, Chun-Quan</au><au>Xu, Li-Yan</au><au>Lin, De-Chen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SEanalysis: a web tool for super-enhancer associated regulatory analysis</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2019-07-02</date><risdate>2019</risdate><volume>47</volume><issue>W1</issue><spage>W248</spage><epage>W255</epage><pages>W248-W255</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31028388</pmid><doi>10.1093/nar/gkz302</doi><orcidid>https://orcid.org/0000-0002-1618-4292</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Nucleic acids research, 2019-07, Vol.47 (W1), p.W248-W255 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Open; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Binding Sites - genetics Databases, Genetic Enhancer Elements, Genetic - genetics Gene Expression Regulation - genetics Gene Regulatory Networks - genetics Humans Internet Software Transcription Factors - genetics Web Server Issue |
| title | SEanalysis: a web tool for super-enhancer associated regulatory analysis |
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