STarMirDB: A database of microRNA binding sites
microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or...
Gespeichert in:
| Veröffentlicht in: | RNA biology 2016-06, Vol.13 (6), p.554-560 |
|---|---|
| Hauptverfasser: | , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 560 |
|---|---|
| container_issue | 6 |
| container_start_page | 554 |
| container_title | RNA biology |
| container_volume | 13 |
| creator | Rennie, William Kanoria, Shaveta Liu, Chaochun Mallick, Bibekanand Long, Dang Wolenc, Adam Carmack, C. Steven Lu, Jun Ding, Ye |
| description | microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at
http://sfold.wadsworth.org/starmirDB.php
. STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3′ UTR, CDS and 5′ UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files. |
| doi_str_mv | 10.1080/15476286.2016.1182279 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_proquest_miscellaneous_1797869135</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2477634132</sourcerecordid><originalsourceid>FETCH-LOGICAL-c501t-ef213d014d1b507c6a8526b6b809ca41537e7b90a544292c348ba54c8aafce1b3</originalsourceid><addsrcrecordid>eNqFkU1P3DAQhi3UCijtTwDl2EsWj7_TQ9Ut9EuirdTC2Ro7DhglMbWzRfz7ZrULohc4eSQ_83o8DyGHQBdADT0GKbRiRi0YBbUAMIzpZofsg5SyNtKIF-ta6HoN7ZFXpVxTypVp5C7ZYxqEMI3eJ8e_zzF_j_n047tqWbU4ocMSqtRVQ_Q5_fqxrFwc2zheViVOobwmLzvsS3izPQ_IxedP5ydf67OfX76dLM9qLylMdegY8JaCaMFJqr1CI5lyyhnaeBQguQ7aNRSlEKxhngvj5tobxM4HcPyAvN_k3qzcEFofxiljb29yHDDf2YTR_n8zxit7mf5a0ah5EXoOeLsNyOnPKpTJDrH40Pc4hrQqlgmtFRfA2bMozHlGNcDljMoNOu-mlBy6h4mA2rUXe-_Frr3YrZe57-jxdx667kXMwIcNEMcu5QFvU-5bO-Fdn3KXcfSxWP70G_8AMSya8g</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1797869135</pqid></control><display><type>article</type><title>STarMirDB: A database of microRNA binding sites</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><creator>Rennie, William ; Kanoria, Shaveta ; Liu, Chaochun ; Mallick, Bibekanand ; Long, Dang ; Wolenc, Adam ; Carmack, C. Steven ; Lu, Jun ; Ding, Ye</creator><creatorcontrib>Rennie, William ; Kanoria, Shaveta ; Liu, Chaochun ; Mallick, Bibekanand ; Long, Dang ; Wolenc, Adam ; Carmack, C. Steven ; Lu, Jun ; Ding, Ye</creatorcontrib><description>microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at
http://sfold.wadsworth.org/starmirDB.php
. STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3′ UTR, CDS and 5′ UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files.</description><identifier>ISSN: 1547-6286</identifier><identifier>ISSN: 1555-8584</identifier><identifier>EISSN: 1555-8584</identifier><identifier>DOI: 10.1080/15476286.2016.1182279</identifier><identifier>PMID: 27144897</identifier><language>eng</language><publisher>United States: Taylor & Francis</publisher><subject>3' Untranslated Regions ; 5' Untranslated Regions ; Animals ; Binding site prediction ; Binding Sites ; Brief Communication ; Caenorhabditis elegans - genetics ; CLIP ; Databases, Nucleic Acid ; Gene Expression Regulation ; Humans ; messenger RNA ; Mice ; microRNA ; MicroRNAs - genetics ; non-coding RNA ; nucleic acid hybridization ; nucleotides ; prediction ; RNA Stability ; RNA, Messenger - chemistry ; RNA, Messenger - genetics ; seed site ; seedless site ; Sequence Analysis, RNA ; Software ; thermodynamics ; transcriptome ; User-Computer Interface</subject><ispartof>RNA biology, 2016-06, Vol.13 (6), p.554-560</ispartof><rights>Published with license by Taylor & Francis © Wadsworth Center 2016</rights><rights>Published with license by Taylor & Francis 2016 Taylor & Francis</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c501t-ef213d014d1b507c6a8526b6b809ca41537e7b90a544292c348ba54c8aafce1b3</citedby><cites>FETCH-LOGICAL-c501t-ef213d014d1b507c6a8526b6b809ca41537e7b90a544292c348ba54c8aafce1b3</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/PMC4962797/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962797/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27915,27916,53782,53784</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27144897$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rennie, William</creatorcontrib><creatorcontrib>Kanoria, Shaveta</creatorcontrib><creatorcontrib>Liu, Chaochun</creatorcontrib><creatorcontrib>Mallick, Bibekanand</creatorcontrib><creatorcontrib>Long, Dang</creatorcontrib><creatorcontrib>Wolenc, Adam</creatorcontrib><creatorcontrib>Carmack, C. Steven</creatorcontrib><creatorcontrib>Lu, Jun</creatorcontrib><creatorcontrib>Ding, Ye</creatorcontrib><title>STarMirDB: A database of microRNA binding sites</title><title>RNA biology</title><addtitle>RNA Biol</addtitle><description>microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at
http://sfold.wadsworth.org/starmirDB.php
. STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3′ UTR, CDS and 5′ UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files.</description><subject>3' Untranslated Regions</subject><subject>5' Untranslated Regions</subject><subject>Animals</subject><subject>Binding site prediction</subject><subject>Binding Sites</subject><subject>Brief Communication</subject><subject>Caenorhabditis elegans - genetics</subject><subject>CLIP</subject><subject>Databases, Nucleic Acid</subject><subject>Gene Expression Regulation</subject><subject>Humans</subject><subject>messenger RNA</subject><subject>Mice</subject><subject>microRNA</subject><subject>MicroRNAs - genetics</subject><subject>non-coding RNA</subject><subject>nucleic acid hybridization</subject><subject>nucleotides</subject><subject>prediction</subject><subject>RNA Stability</subject><subject>RNA, Messenger - chemistry</subject><subject>RNA, Messenger - genetics</subject><subject>seed site</subject><subject>seedless site</subject><subject>Sequence Analysis, RNA</subject><subject>Software</subject><subject>thermodynamics</subject><subject>transcriptome</subject><subject>User-Computer Interface</subject><issn>1547-6286</issn><issn>1555-8584</issn><issn>1555-8584</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>0YH</sourceid><sourceid>EIF</sourceid><recordid>eNqFkU1P3DAQhi3UCijtTwDl2EsWj7_TQ9Ut9EuirdTC2Ro7DhglMbWzRfz7ZrULohc4eSQ_83o8DyGHQBdADT0GKbRiRi0YBbUAMIzpZofsg5SyNtKIF-ta6HoN7ZFXpVxTypVp5C7ZYxqEMI3eJ8e_zzF_j_n047tqWbU4ocMSqtRVQ_Q5_fqxrFwc2zheViVOobwmLzvsS3izPQ_IxedP5ydf67OfX76dLM9qLylMdegY8JaCaMFJqr1CI5lyyhnaeBQguQ7aNRSlEKxhngvj5tobxM4HcPyAvN_k3qzcEFofxiljb29yHDDf2YTR_n8zxit7mf5a0ah5EXoOeLsNyOnPKpTJDrH40Pc4hrQqlgmtFRfA2bMozHlGNcDljMoNOu-mlBy6h4mA2rUXe-_Frr3YrZe57-jxdx667kXMwIcNEMcu5QFvU-5bO-Fdn3KXcfSxWP70G_8AMSya8g</recordid><startdate>20160602</startdate><enddate>20160602</enddate><creator>Rennie, William</creator><creator>Kanoria, Shaveta</creator><creator>Liu, Chaochun</creator><creator>Mallick, Bibekanand</creator><creator>Long, Dang</creator><creator>Wolenc, Adam</creator><creator>Carmack, C. Steven</creator><creator>Lu, Jun</creator><creator>Ding, Ye</creator><general>Taylor & Francis</general><scope>0YH</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>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20160602</creationdate><title>STarMirDB: A database of microRNA binding sites</title><author>Rennie, William ; Kanoria, Shaveta ; Liu, Chaochun ; Mallick, Bibekanand ; Long, Dang ; Wolenc, Adam ; Carmack, C. Steven ; Lu, Jun ; Ding, Ye</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c501t-ef213d014d1b507c6a8526b6b809ca41537e7b90a544292c348ba54c8aafce1b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>3' Untranslated Regions</topic><topic>5' Untranslated Regions</topic><topic>Animals</topic><topic>Binding site prediction</topic><topic>Binding Sites</topic><topic>Brief Communication</topic><topic>Caenorhabditis elegans - genetics</topic><topic>CLIP</topic><topic>Databases, Nucleic Acid</topic><topic>Gene Expression Regulation</topic><topic>Humans</topic><topic>messenger RNA</topic><topic>Mice</topic><topic>microRNA</topic><topic>MicroRNAs - genetics</topic><topic>non-coding RNA</topic><topic>nucleic acid hybridization</topic><topic>nucleotides</topic><topic>prediction</topic><topic>RNA Stability</topic><topic>RNA, Messenger - chemistry</topic><topic>RNA, Messenger - genetics</topic><topic>seed site</topic><topic>seedless site</topic><topic>Sequence Analysis, RNA</topic><topic>Software</topic><topic>thermodynamics</topic><topic>transcriptome</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rennie, William</creatorcontrib><creatorcontrib>Kanoria, Shaveta</creatorcontrib><creatorcontrib>Liu, Chaochun</creatorcontrib><creatorcontrib>Mallick, Bibekanand</creatorcontrib><creatorcontrib>Long, Dang</creatorcontrib><creatorcontrib>Wolenc, Adam</creatorcontrib><creatorcontrib>Carmack, C. Steven</creatorcontrib><creatorcontrib>Lu, Jun</creatorcontrib><creatorcontrib>Ding, Ye</creatorcontrib><collection>Taylor & Francis Open Access</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>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rennie, William</au><au>Kanoria, Shaveta</au><au>Liu, Chaochun</au><au>Mallick, Bibekanand</au><au>Long, Dang</au><au>Wolenc, Adam</au><au>Carmack, C. Steven</au><au>Lu, Jun</au><au>Ding, Ye</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>STarMirDB: A database of microRNA binding sites</atitle><jtitle>RNA biology</jtitle><addtitle>RNA Biol</addtitle><date>2016-06-02</date><risdate>2016</risdate><volume>13</volume><issue>6</issue><spage>554</spage><epage>560</epage><pages>554-560</pages><issn>1547-6286</issn><issn>1555-8584</issn><eissn>1555-8584</eissn><abstract>microRNAs (miRNAs) are an abundant class of small endogenous non-coding RNAs (ncRNAs) of ∼22 nucleotides (nts) in length. These small regulatory molecules are involved in diverse developmental, physiological and pathological processes. miRNAs target mRNAs (mRNAs) for translational repression and/or mRNA degradation. Predictions of miRNA binding sites facilitate experimental validation of miRNA targets. Models developed with data from CLIP studies have been used for predictions of miRNA binding sites in the whole transcriptomes of human, mouse and worm. The prediction results have been assembled into STarMirDB, a new database of miRNA binding sites available at
http://sfold.wadsworth.org/starmirDB.php
. STarMirDB can be searched by miRNAs or mRNAs separately or in combination. The search results are categorized into seed and seedless sites in 3′ UTR, CDS and 5′ UTR. For each predicted site, STarMirDB provides a comprehensive list of sequence, thermodynamic and target structural features that are known to influence miRNA: target interaction. A high resolution PDF diagram of the conformation of the miRNA:target hybrid is also available for visualization and publication. The results of a database search are available through both an interactive viewer and downloadable text files.</abstract><cop>United States</cop><pub>Taylor & Francis</pub><pmid>27144897</pmid><doi>10.1080/15476286.2016.1182279</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1547-6286 |
| ispartof | RNA biology, 2016-06, Vol.13 (6), p.554-560 |
| issn | 1547-6286 1555-8584 1555-8584 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1797869135 |
| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | 3' Untranslated Regions 5' Untranslated Regions Animals Binding site prediction Binding Sites Brief Communication Caenorhabditis elegans - genetics CLIP Databases, Nucleic Acid Gene Expression Regulation Humans messenger RNA Mice microRNA MicroRNAs - genetics non-coding RNA nucleic acid hybridization nucleotides prediction RNA Stability RNA, Messenger - chemistry RNA, Messenger - genetics seed site seedless site Sequence Analysis, RNA Software thermodynamics transcriptome User-Computer Interface |
| title | STarMirDB: A database of microRNA binding sites |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-15T04%3A55%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=STarMirDB:%20A%20database%20of%20microRNA%20binding%20sites&rft.jtitle=RNA%20biology&rft.au=Rennie,%20William&rft.date=2016-06-02&rft.volume=13&rft.issue=6&rft.spage=554&rft.epage=560&rft.pages=554-560&rft.issn=1547-6286&rft.eissn=1555-8584&rft_id=info:doi/10.1080/15476286.2016.1182279&rft_dat=%3Cproquest_pubme%3E2477634132%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1797869135&rft_id=info:pmid/27144897&rfr_iscdi=true |