HPIDB - a unified resource for host-pathogen interactions
Identifieur interne : 000167 ( Ncbi/Merge ); précédent : 000166; suivant : 000168HPIDB - a unified resource for host-pathogen interactions
Auteurs : Ranjit Kumar [États-Unis] ; Bindu Nanduri [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens.
Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database.
HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at
Url:
DOI: 10.1186/1471-2105-11-S6-S16
PubMed: 20946599
PubMed Central: 3026363
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a unified resource for host-pathogen interactions</title><author><name sortKey="Kumar, Ranjit" sort="Kumar, Ranjit" uniqKey="Kumar R" first="Ranjit" last="Kumar">Ranjit Kumar</name><affiliation wicri:level="2"><nlm:aff id="I1">College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762</wicri:regionArea><placeName><region type="state">État du Mississippi</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762</wicri:regionArea><placeName><region type="state">État du Mississippi</region></placeName></affiliation></author><author><name sortKey="Nanduri, Bindu" sort="Nanduri, Bindu" uniqKey="Nanduri B" first="Bindu" last="Nanduri">Bindu Nanduri</name><affiliation wicri:level="2"><nlm:aff id="I1">College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762</wicri:regionArea><placeName><region type="state">État du Mississippi</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762</wicri:regionArea><placeName><region type="state">État du Mississippi</region></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens.</p></sec><sec><title>Results</title><p>Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database. </p></sec><sec><title>Conclusions</title><p>HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at <ext-link ext-link-type="uri" xlink:href="http://agbase.msstate.edu/hpi/main.html">http://agbase.msstate.edu/hpi/main.html</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Guldener, U" uniqKey="Guldener U">U Guldener</name></author><author><name sortKey="Munsterkotter, M" uniqKey="Munsterkotter M">M Munsterkotter</name></author><author><name sortKey="Oesterheld, M" uniqKey="Oesterheld M">M Oesterheld</name></author><author><name sortKey="Pagel, P" uniqKey="Pagel P">P Pagel</name></author><author><name sortKey="Ruepp, A" uniqKey="Ruepp A">A Ruepp</name></author><author><name sortKey="Mewes, Hw" uniqKey="Mewes H">HW Mewes</name></author><author><name sortKey="Stumpflen, V" uniqKey="Stumpflen V">V Stumpflen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keshava Prasad, Ts" uniqKey="Keshava Prasad T">TS Keshava Prasad</name></author><author><name 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article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id><journal-title-group><journal-title>BMC Bioinformatics</journal-title></journal-title-group><issn pub-type="epub">1471-2105</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20946599</article-id><article-id pub-id-type="pmc">3026363</article-id><article-id pub-id-type="publisher-id">1471-2105-11-S6-S16</article-id><article-id pub-id-type="doi">10.1186/1471-2105-11-S6-S16</article-id><article-categories><subj-group subj-group-type="heading"><subject>Proceedings</subject></subj-group></article-categories><title-group><article-title>HPIDB - a unified resource for host-pathogen interactions</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Kumar</surname><given-names>Ranjit</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><email>rkumar@cvm.msstate.edu</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Nanduri</surname><given-names>Bindu</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><email>bnanduri@cvm.msstate.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA</aff><aff id="I2"><label>2</label>Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA</aff><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>7</day><month>10</month><year>2010</year></pub-date><volume>11</volume><issue>Suppl 6</issue><supplement><named-content content-type="supplement-title">Proceedings of the Seventh Annual MCBIOS Conference. Bioinformatics: Systems, Biology, Informatics and Computation</named-content><named-content content-type="supplement-editor">Jonathan D Wren (Senior Editor), Dan Berleant, Susan M Bridges, Doris M Kupfer and Edward J Perkins</named-content></supplement><fpage>S16</fpage><lpage>S16</lpage><permissions><copyright-statement>Copyright ©2010 Kumar and Nanduri; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2010</copyright-year><copyright-holder>Kumar and Nanduri; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.biomedcentral.com/1471-2105/11/S6/S16"></self-uri><abstract><sec><title>Background</title><p>Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens.</p></sec><sec><title>Results</title><p>Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database. </p></sec><sec><title>Conclusions</title><p>HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at <ext-link ext-link-type="uri" xlink:href="http://agbase.msstate.edu/hpi/main.html">http://agbase.msstate.edu/hpi/main.html</ext-link>.</p></sec></abstract><conference><conf-date>19–20 February 2010</conf-date><conf-name>Seventh Annual MCBIOS Conference. Bioinformatics: Systems, Biology, Informatics and Computation</conf-name><conf-loc>Jonesboro, AR, USA</conf-loc></conference></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>État du Mississippi</li></region></list><tree><country name="États-Unis"><region name="État du Mississippi"><name sortKey="Kumar, Ranjit" sort="Kumar, Ranjit" uniqKey="Kumar R" first="Ranjit" last="Kumar">Ranjit Kumar</name></region><name sortKey="Kumar, Ranjit" sort="Kumar, Ranjit" uniqKey="Kumar R" first="Ranjit" last="Kumar">Ranjit Kumar</name><name sortKey="Nanduri, Bindu" sort="Nanduri, Bindu" uniqKey="Nanduri B" first="Bindu" last="Nanduri">Bindu Nanduri</name><name sortKey="Nanduri, Bindu" sort="Nanduri, Bindu" uniqKey="Nanduri B" first="Bindu" last="Nanduri">Bindu Nanduri</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|étape= Merge
|type= RBID
|clé= PMC:3026363
|texte= HPIDB - a unified resource for host-pathogen interactions
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:20946599" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |