CovidV1, PubMed, Corpus, bibRecord, 000666

VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.

Identifieur interne : 000666 ( PubMed/Corpus ); précédent : 000665; suivant : 000667

VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.

Auteurs : Nishant Thakur ; Abid Qureshi ; Manoj Kumar

Source :

Nucleic acids research [ 1362-4962 ] ; 2012.

RBID : pubmed:22139916

English descriptors

KwdEn :
- Databases, Nucleic Acid, Genome, Viral, RNA Interference, RNA, Small Interfering (chemistry), Software.
MESH :
- chemical , chemistry : RNA, Small Interfering.
- Databases, Nucleic Acid, Genome, Viral, RNA Interference, Software.

Abstract

RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.

DOI: 10.1093/nar/gkr1147
PubMed: 22139916

Links to Exploration step

pubmed:22139916

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.</title>
<author><name sortKey="Thakur, Nishant" sort="Thakur, Nishant" uniqKey="Thakur N" first="Nishant" last="Thakur">Nishant Thakur</name>
<affiliation><nlm:affiliation>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036, India.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Qureshi, Abid" sort="Qureshi, Abid" uniqKey="Qureshi A" first="Abid" last="Qureshi">Abid Qureshi</name>
</author>
<author><name sortKey="Kumar, Manoj" sort="Kumar, Manoj" uniqKey="Kumar M" first="Manoj" last="Kumar">Manoj Kumar</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2012">2012</date>
<idno type="RBID">pubmed:22139916</idno>
<idno type="pmid">22139916</idno>
<idno type="doi">10.1093/nar/gkr1147</idno>
<idno type="wicri:Area/PubMed/Corpus">000666</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000666</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.</title>
<author><name sortKey="Thakur, Nishant" sort="Thakur, Nishant" uniqKey="Thakur N" first="Nishant" last="Thakur">Nishant Thakur</name>
<affiliation><nlm:affiliation>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036, India.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Qureshi, Abid" sort="Qureshi, Abid" uniqKey="Qureshi A" first="Abid" last="Qureshi">Abid Qureshi</name>
</author>
<author><name sortKey="Kumar, Manoj" sort="Kumar, Manoj" uniqKey="Kumar M" first="Manoj" last="Kumar">Manoj Kumar</name>
</author>
</analytic>
<series><title level="j">Nucleic acids research</title>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2012" type="published">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Nucleic Acid</term>
<term>Genome, Viral</term>
<term>RNA Interference</term>
<term>RNA, Small Interfering (chemistry)</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Small Interfering</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term>
<term>Genome, Viral</term>
<term>RNA Interference</term>
<term>Software</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22139916</PMID>
<DateCompleted><Year>2012</Year>
<Month>07</Month>
<Day>05</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>40</Volume>
<Issue>Database issue</Issue>
<PubDate><Year>2012</Year>
<Month>Jan</Month>
</PubDate>
</JournalIssue>
<Title>Nucleic acids research</Title>
<ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation>
</Journal>
<ArticleTitle>VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.</ArticleTitle>
<Pagination><MedlinePgn>D230-6</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkr1147</ELocationID>
<Abstract><AbstractText>RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Thakur</LastName>
<ForeName>Nishant</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036, India.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Qureshi</LastName>
<ForeName>Abid</ForeName>
<Initials>A</Initials>
</Author>
<Author ValidYN="Y"><LastName>Kumar</LastName>
<ForeName>Manoj</ForeName>
<Initials>M</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2011</Year>
<Month>12</Month>
<Day>01</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Nucleic Acids Res</MedlineTA>
<NlmUniqueID>0411011</NlmUniqueID>
<ISSNLinking>0305-1048</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D034741">RNA, Small Interfering</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D034622" MajorTopicYN="Y">RNA Interference</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D034741" MajorTopicYN="N">RNA, Small Interfering</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012984" MajorTopicYN="N">Software</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2011</Year>
<Month>12</Month>
<Day>6</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2011</Year>
<Month>12</Month>
<Day>6</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2012</Year>
<Month>7</Month>
<Day>6</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">22139916</ArticleId>
<ArticleId IdType="pii">gkr1147</ArticleId>
<ArticleId IdType="doi">10.1093/nar/gkr1147</ArticleId>
<ArticleId IdType="pmc">PMC3245049</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Retrovirology. 2007;4:80</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17996047</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Ther. 2008 Mar;16(3):557-64</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18180777</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2006 Apr 15;22(8):1027-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16443930</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12411-2</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11035785</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Silence. 2010 Jul 08;1(1):14</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20615220</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Pharm Res. 2011 Dec;28(12):2966-82</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21826573</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Sci Transl Med. 2010 Jun 16;2(36):36ra43</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20555022</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Hum Gene Ther. 2008 May;19(5):451-62</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18435603</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Biotechnol. 2007 Dec;25(12):1435-43</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18066040</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BioDrugs. 2009;23(5):305-32</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19754220</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 1998 Feb 19;391(6669):806-11</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9486653</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>RNA. 2008 May;14(5):853-61</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18367722</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Genet. 2011 May;12(5):329-40</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21499294</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 2005 Jun;79(11):7050-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15890944</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Methods Mol Biol. 2009;555:43-61</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19495687</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biochem Biophys Res Commun. 2008 Nov 14;376(2):389-94</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18793610</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Viral Hepat. 2006 Nov;13(11):756-61</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17052275</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Int J Biol Macromol. 2006 Feb 28;38(1):65-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16448692</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Rev Clin Exp Hematol. 2003 Sep;7(3):270-91</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15024970</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2005 Jan 1;33(Database issue):D108-11</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15608157</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Cell. 2005 Jul 15;122(1):17-20</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16009129</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS One. 2011;6(10):e25917</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22022467</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Comput Appl Biosci. 1988 Mar;4(1):11-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">3382986</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W448-50</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16845046</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Gene Ther. 2006 Mar;13(6):532-40</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16177819</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2010 May 11;107(19):8800-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20421463</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Drug News Perspect. 2010 Jul-Aug;23(6):341-50</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20697601</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Methods. 2006 Mar;3(3):199-204</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16489337</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>N Engl J Med. 2004 Oct 21;351(17):1772-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15496626</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Trends Genet. 2000 Jun;16(6):276-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10827456</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2008 May 15;24(10):1316-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18397893</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation>
<ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Cell Res. 2005 Mar;15(3):193-200</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15780182</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Drug Target. 2008 Feb;16(2):140-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18274934</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Genet. 2010 Dec;89(4):527-37</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21273705</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2010 Jan 8;327(5962):198-201</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19965718</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Hepatology. 2003 Oct;38(4):842-50</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14512871</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2005 Jan 1;33(Database issue):D131-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15608162</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Drug Discov. 2010 Jan;9(1):57-67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20043028</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Handb Exp Pharmacol. 2009;(189):243-63</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19048203</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Virol. 2004 Mar;78(5):2601-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14963165</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Biotechnol. 2003 Jun;21(6):635-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12754523</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2718-23</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12594334</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Genet. 2008 Apr;9(4):267-76</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18319742</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2008 Dec;36(22):7100-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18988625</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2003 Jul 1;31(13):3406-15</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12824337</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV1/Data/PubMed/Corpus

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000666 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 000666 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Sante
   |area=    CovidV1
   |flux=    PubMed
   |étape=   Corpus
   |type=    RBID
   |clé=     pubmed:22139916
   |texte=   VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i   -Sk "pubmed:22139916" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd   \
       | NlmPubMed2Wicri -a CovidV1

This area was generated with Dilib version V0.6.33.
Data generation: Fri Mar 27 18:14:15 2020. Site generation: Sun Jan 31 15:15:08 2021

	Serveur d'exploration Covid
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration Covid

VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.

VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki