miRTargetLink 2.0—interactive miRNA target gene and target pathway networks
Abstract Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without com...
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| Veröffentlicht in: | Nucleic acids research 2021-07, Vol.49 (W1), p.W409-W416 |
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| container_title | Nucleic acids research |
| container_volume | 49 |
| creator | Kern, Fabian Aparicio-Puerta, Ernesto Li, Yongping Fehlmann, Tobias Kehl, Tim Wagner, Viktoria Ray, Kamalika Ludwig, Nicole Lenhof, Hans-Peter Meese, Eckart Keller, Andreas |
| description | Abstract
Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
Graphical Abstract
Graphical abstract
MiRTargetLink 2.0 offers interactive, web-based functionality to dissect networks of miRNAs and their target genes and pathways in three commonly investigated species. |
| doi_str_mv | 10.1093/nar/gkab297 |
| format | Article |
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Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
Graphical Abstract
Graphical abstract
MiRTargetLink 2.0 offers interactive, web-based functionality to dissect networks of miRNAs and their target genes and pathways in three commonly investigated species.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkab297</identifier><identifier>PMID: 34009375</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Aniridia - genetics ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Mice ; MicroRNAs - metabolism ; Rats ; Software ; Web Server Issue</subject><ispartof>Nucleic acids research, 2021-07, Vol.49 (W1), p.W409-W416</ispartof><rights>The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c478t-923cb81b8f5d636f349761321428d4880ce28013dcc86b4c47dedf7122039aba3</citedby><cites>FETCH-LOGICAL-c478t-923cb81b8f5d636f349761321428d4880ce28013dcc86b4c47dedf7122039aba3</cites><orcidid>0000-0002-5361-0895 ; 0000-0003-1967-2918 ; 0000-0002-8223-3750 ; 0000-0002-9523-7566</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/PMC8262750/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262750/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34009375$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kern, Fabian</creatorcontrib><creatorcontrib>Aparicio-Puerta, Ernesto</creatorcontrib><creatorcontrib>Li, Yongping</creatorcontrib><creatorcontrib>Fehlmann, Tobias</creatorcontrib><creatorcontrib>Kehl, Tim</creatorcontrib><creatorcontrib>Wagner, Viktoria</creatorcontrib><creatorcontrib>Ray, Kamalika</creatorcontrib><creatorcontrib>Ludwig, Nicole</creatorcontrib><creatorcontrib>Lenhof, Hans-Peter</creatorcontrib><creatorcontrib>Meese, Eckart</creatorcontrib><creatorcontrib>Keller, Andreas</creatorcontrib><title>miRTargetLink 2.0—interactive miRNA target gene and target pathway networks</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
Graphical Abstract
Graphical abstract
MiRTargetLink 2.0 offers interactive, web-based functionality to dissect networks of miRNAs and their target genes and pathways in three commonly investigated species.</description><subject>Animals</subject><subject>Aniridia - genetics</subject><subject>Gene Expression Regulation</subject><subject>Gene Regulatory Networks</subject><subject>Humans</subject><subject>Mice</subject><subject>MicroRNAs - metabolism</subject><subject>Rats</subject><subject>Software</subject><subject>Web Server Issue</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kctKw0AUhgdRbK2u3EtWIkjauWUy2QileIOqIHU9TCaTNjaZ1JlpS3c-hE_okxjtBd24OhzO9__ncH4AThHsIpiQnpG2N57KFCfxHmgjwnBIE4b3QRsSGIUIUt4CR869QogoiughaBEKG2UctcFDVTyPpB1rPyzMNMBd-Pn-URivrVS-WOigmT_2A_-DBGNtdCBNtu1n0k-WchUY7Ze1nbpjcJDL0umTTe2Al5vr0eAuHD7d3g_6w1DRmPswwUSlHKU8jzJGWE5oEjNEMKKYZ5RzqDTmEJFMKc5S2ogyneUxwhiSRKaSdMDV2nc2TyudKW28laWY2aKSdiVqWYi_E1NMxLheCI4ZjiPYGFxsDGz9NtfOi6pwSpelNLqeO4EjzBPIGKMNerlGla2dszrfrUFQfAcgmgDEJoCGPvt92Y7dfrwBztdAPZ_96_QFc4aQzw</recordid><startdate>20210702</startdate><enddate>20210702</enddate><creator>Kern, Fabian</creator><creator>Aparicio-Puerta, Ernesto</creator><creator>Li, Yongping</creator><creator>Fehlmann, Tobias</creator><creator>Kehl, Tim</creator><creator>Wagner, Viktoria</creator><creator>Ray, Kamalika</creator><creator>Ludwig, Nicole</creator><creator>Lenhof, Hans-Peter</creator><creator>Meese, Eckart</creator><creator>Keller, Andreas</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/0000-0002-5361-0895</orcidid><orcidid>https://orcid.org/0000-0003-1967-2918</orcidid><orcidid>https://orcid.org/0000-0002-8223-3750</orcidid><orcidid>https://orcid.org/0000-0002-9523-7566</orcidid></search><sort><creationdate>20210702</creationdate><title>miRTargetLink 2.0—interactive miRNA target gene and target pathway networks</title><author>Kern, Fabian ; Aparicio-Puerta, Ernesto ; Li, Yongping ; Fehlmann, Tobias ; Kehl, Tim ; Wagner, Viktoria ; Ray, Kamalika ; Ludwig, Nicole ; Lenhof, Hans-Peter ; Meese, Eckart ; Keller, Andreas</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c478t-923cb81b8f5d636f349761321428d4880ce28013dcc86b4c47dedf7122039aba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Aniridia - genetics</topic><topic>Gene Expression Regulation</topic><topic>Gene Regulatory Networks</topic><topic>Humans</topic><topic>Mice</topic><topic>MicroRNAs - metabolism</topic><topic>Rats</topic><topic>Software</topic><topic>Web Server Issue</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kern, Fabian</creatorcontrib><creatorcontrib>Aparicio-Puerta, Ernesto</creatorcontrib><creatorcontrib>Li, Yongping</creatorcontrib><creatorcontrib>Fehlmann, Tobias</creatorcontrib><creatorcontrib>Kehl, Tim</creatorcontrib><creatorcontrib>Wagner, Viktoria</creatorcontrib><creatorcontrib>Ray, Kamalika</creatorcontrib><creatorcontrib>Ludwig, Nicole</creatorcontrib><creatorcontrib>Lenhof, Hans-Peter</creatorcontrib><creatorcontrib>Meese, Eckart</creatorcontrib><creatorcontrib>Keller, Andreas</creatorcontrib><collection>Oxford Journals Open Access Collection</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>Kern, Fabian</au><au>Aparicio-Puerta, Ernesto</au><au>Li, Yongping</au><au>Fehlmann, Tobias</au><au>Kehl, Tim</au><au>Wagner, Viktoria</au><au>Ray, Kamalika</au><au>Ludwig, Nicole</au><au>Lenhof, Hans-Peter</au><au>Meese, Eckart</au><au>Keller, Andreas</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>miRTargetLink 2.0—interactive miRNA target gene and target pathway networks</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2021-07-02</date><risdate>2021</risdate><volume>49</volume><issue>W1</issue><spage>W409</spage><epage>W416</epage><pages>W409-W416</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>Abstract
Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
Graphical Abstract
Graphical abstract
MiRTargetLink 2.0 offers interactive, web-based functionality to dissect networks of miRNAs and their target genes and pathways in three commonly investigated species.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34009375</pmid><doi>10.1093/nar/gkab297</doi><orcidid>https://orcid.org/0000-0002-5361-0895</orcidid><orcidid>https://orcid.org/0000-0003-1967-2918</orcidid><orcidid>https://orcid.org/0000-0002-8223-3750</orcidid><orcidid>https://orcid.org/0000-0002-9523-7566</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2021-07, Vol.49 (W1), p.W409-W416 |
| issn | 0305-1048 1362-4962 1362-4962 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8262750 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Aniridia - genetics Gene Expression Regulation Gene Regulatory Networks Humans Mice MicroRNAs - metabolism Rats Software Web Server Issue |
| title | miRTargetLink 2.0—interactive miRNA target gene and target pathway networks |
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