DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data
Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transc...
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| Veröffentlicht in: | Nucleic acids research 2016-07, Vol.44 (W1), p.W128-W134 |
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| creator | Vlachos, Ioannis S Vergoulis, Thanasis Paraskevopoulou, Maria D Lykokanellos, Filopoimin Georgakilas, Georgios Georgiou, Penny Chatzopoulos, Serafeim Karagkouni, Dimitra Christodoulou, Foteini Dalamagas, Theodore Hatzigeorgiou, Artemis G |
| description | Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement. |
| doi_str_mv | 10.1093/nar/gkw455 |
| format | Article |
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DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkw455</identifier><identifier>PMID: 27207881</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Binding Sites ; Caenorhabditis elegans - genetics ; Caenorhabditis elegans - metabolism ; Drosophila melanogaster - genetics ; Drosophila melanogaster - metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Internet ; Mice ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Molecular Sequence Annotation ; Nematoda ; Protein Binding ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Sequence Analysis, RNA ; Signal Transduction ; Software ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription, Genetic ; Web Server issue</subject><ispartof>Nucleic acids research, 2016-07, Vol.44 (W1), p.W128-W134</ispartof><rights>The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c411t-e9fa7ac921075581afe7188d43badf1044f51277779b576164bd933630194f753</citedby><cites>FETCH-LOGICAL-c411t-e9fa7ac921075581afe7188d43badf1044f51277779b576164bd933630194f753</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/PMC4987956/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987956/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27207881$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vlachos, Ioannis S</creatorcontrib><creatorcontrib>Vergoulis, Thanasis</creatorcontrib><creatorcontrib>Paraskevopoulou, Maria D</creatorcontrib><creatorcontrib>Lykokanellos, Filopoimin</creatorcontrib><creatorcontrib>Georgakilas, Georgios</creatorcontrib><creatorcontrib>Georgiou, Penny</creatorcontrib><creatorcontrib>Chatzopoulos, Serafeim</creatorcontrib><creatorcontrib>Karagkouni, Dimitra</creatorcontrib><creatorcontrib>Christodoulou, Foteini</creatorcontrib><creatorcontrib>Dalamagas, Theodore</creatorcontrib><creatorcontrib>Hatzigeorgiou, Artemis G</creatorcontrib><title>DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.</description><subject>Animals</subject><subject>Binding Sites</subject><subject>Caenorhabditis elegans - genetics</subject><subject>Caenorhabditis elegans - metabolism</subject><subject>Drosophila melanogaster - genetics</subject><subject>Drosophila melanogaster - metabolism</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation</subject><subject>Humans</subject><subject>Internet</subject><subject>Mice</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Molecular Sequence Annotation</subject><subject>Nematoda</subject><subject>Protein Binding</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Sequence Analysis, RNA</subject><subject>Signal Transduction</subject><subject>Software</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription, Genetic</subject><subject>Web Server issue</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU9PGzEQxS3UqgTaCx-g8rFCWvCs7bXdQ6WI_xIKEoWz5Xi9wWXXDvYm0G9fo1AEN-Yyh_np6b15CO0BOQCi6GEw6XBx_8g430IToE1dMdXUn9CEUMIrIExuo52c_xACDDj7grZrURMhJUzQcHwxnU2rwaeTp5tk8Lo-ID_xbbBx7ZIPCzx4m-L1bJqxCS0ekwnZJr8cfQy4M3aMKeNHP95hm1bWmx6n2LuMfcCzs9_YPS2Ty_kZbs1ovqLPnemz-_ayd9Ht6cnN0Xl1eXV2cTS9rCwDGCunOiOMVTUQwbkE0zkBUraMzk3blUCs41CLMmrORQMNm7eK0oYSUKwTnO6iXxvd5Wo-uNa6UIz3epn8YNJfHY3X7y_B3-lFXGumpFC8KQI_XgRSfFi5POrBZ-v63gQXV1mDJLIp9pj6CEqFIpSKgu5v0PLSnJPrXh0B0c9V6lKl3lRZ4O9vM7yi_7uj_wDVJZqx</recordid><startdate>20160708</startdate><enddate>20160708</enddate><creator>Vlachos, Ioannis S</creator><creator>Vergoulis, Thanasis</creator><creator>Paraskevopoulou, Maria D</creator><creator>Lykokanellos, Filopoimin</creator><creator>Georgakilas, Georgios</creator><creator>Georgiou, Penny</creator><creator>Chatzopoulos, Serafeim</creator><creator>Karagkouni, Dimitra</creator><creator>Christodoulou, Foteini</creator><creator>Dalamagas, Theodore</creator><creator>Hatzigeorgiou, Artemis G</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>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20160708</creationdate><title>DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data</title><author>Vlachos, Ioannis S ; Vergoulis, Thanasis ; Paraskevopoulou, Maria D ; Lykokanellos, Filopoimin ; Georgakilas, Georgios ; Georgiou, Penny ; Chatzopoulos, Serafeim ; Karagkouni, Dimitra ; Christodoulou, Foteini ; Dalamagas, Theodore ; Hatzigeorgiou, Artemis G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c411t-e9fa7ac921075581afe7188d43badf1044f51277779b576164bd933630194f753</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Animals</topic><topic>Binding Sites</topic><topic>Caenorhabditis elegans - genetics</topic><topic>Caenorhabditis elegans - metabolism</topic><topic>Drosophila melanogaster - genetics</topic><topic>Drosophila melanogaster - metabolism</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation</topic><topic>Humans</topic><topic>Internet</topic><topic>Mice</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>Molecular Sequence Annotation</topic><topic>Nematoda</topic><topic>Protein Binding</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Sequence Analysis, RNA</topic><topic>Signal Transduction</topic><topic>Software</topic><topic>Transcription Factors - genetics</topic><topic>Transcription Factors - metabolism</topic><topic>Transcription, Genetic</topic><topic>Web Server issue</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vlachos, Ioannis S</creatorcontrib><creatorcontrib>Vergoulis, Thanasis</creatorcontrib><creatorcontrib>Paraskevopoulou, Maria D</creatorcontrib><creatorcontrib>Lykokanellos, Filopoimin</creatorcontrib><creatorcontrib>Georgakilas, Georgios</creatorcontrib><creatorcontrib>Georgiou, Penny</creatorcontrib><creatorcontrib>Chatzopoulos, Serafeim</creatorcontrib><creatorcontrib>Karagkouni, Dimitra</creatorcontrib><creatorcontrib>Christodoulou, Foteini</creatorcontrib><creatorcontrib>Dalamagas, Theodore</creatorcontrib><creatorcontrib>Hatzigeorgiou, Artemis G</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>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</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>Vlachos, Ioannis S</au><au>Vergoulis, Thanasis</au><au>Paraskevopoulou, Maria D</au><au>Lykokanellos, Filopoimin</au><au>Georgakilas, Georgios</au><au>Georgiou, Penny</au><au>Chatzopoulos, Serafeim</au><au>Karagkouni, Dimitra</au><au>Christodoulou, Foteini</au><au>Dalamagas, Theodore</au><au>Hatzigeorgiou, Artemis G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2016-07-08</date><risdate>2016</risdate><volume>44</volume><issue>W1</issue><spage>W128</spage><epage>W134</epage><pages>W128-W134</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>27207881</pmid><doi>10.1093/nar/gkw455</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Binding Sites Caenorhabditis elegans - genetics Caenorhabditis elegans - metabolism Drosophila melanogaster - genetics Drosophila melanogaster - metabolism Gene Expression Profiling Gene Expression Regulation Humans Internet Mice MicroRNAs - genetics MicroRNAs - metabolism Molecular Sequence Annotation Nematoda Protein Binding RNA, Messenger - genetics RNA, Messenger - metabolism Sequence Analysis, RNA Signal Transduction Software Transcription Factors - genetics Transcription Factors - metabolism Transcription, Genetic Web Server issue |
| title | DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data |
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