HPIDB--a unified resource for host-pathogen interactions

doi:10.1186/1471-2105-11-S6-S16

. 2010 Oct 7;11 Suppl 6(Suppl 6):S16.

doi: 10.1186/1471-2105-11-S6-S16.

HPIDB--a unified resource for host-pathogen interactions

Ranjit Kumar¹, Bindu Nanduri

Affiliations

PMID: 20946599
PMCID: PMC3026363
DOI: 10.1186/1471-2105-11-S6-S16

HPIDB--a unified resource for host-pathogen interactions

Ranjit Kumar et al. BMC Bioinformatics. 2010.

. 2010 Oct 7;11 Suppl 6(Suppl 6):S16.

doi: 10.1186/1471-2105-11-S6-S16.

Authors

Ranjit Kumar¹, Bindu Nanduri

Affiliation

¹ College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA. rkumar@cvm.msstate.edu

PMID: 20946599
PMCID: PMC3026363
DOI: 10.1186/1471-2105-11-S6-S16

Abstract

Background: 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.

Results: 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.

Conclusions: 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 http://agbase.msstate.edu/hpi/main.html.

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Figures

**Figure 1**
**Workflow for the construction of HPIDB.** This diagram illustrates data retrieval from various databases, parsing, storage and usage. It also includes a web based user interface which interacts with database.

**Figure 2**
Distribution of PPIs from various databases present in HPIDB.

See this image and copyright information in PMC

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References

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1. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J. et al.The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009;38(Database issue):D525–531. - PMC - PubMed
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[1] Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006;34(Database issue):D436–441. doi: 10.1093/nar/gkj003. - DOI - PMC - PubMed

[2] Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006;34(Database issue):D436–441. doi: 10.1093/nar/gkj003. - DOI - PMC - PubMed

[3] Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A. et al.Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009;37(Database issue):D767–772. doi: 10.1093/nar/gkn892. - DOI - PMC - PubMed

[4] Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A. et al.Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009;37(Database issue):D767–772. doi: 10.1093/nar/gkn892. - DOI - PMC - PubMed

[5] Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004;32(Database issue):D449–451. doi: 10.1093/nar/gkh086. - DOI - PMC - PubMed

[6] Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004;32(Database issue):D449–451. doi: 10.1093/nar/gkh086. - DOI - PMC - PubMed

[7] Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J. et al.The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009;38(Database issue):D525–531. - PMC - PubMed

[8] Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J. et al.The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009;38(Database issue):D525–531. - PMC - PubMed

[9] Gilbert D. Biomolecular interaction network database. Brief Bioinform. 2005;6(2):194–198. doi: 10.1093/bib/6.2.194. - DOI - PubMed

[10] Gilbert D. Biomolecular interaction network database. Brief Bioinform. 2005;6(2):194–198. doi: 10.1093/bib/6.2.194. - DOI - PubMed

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HPIDB--a unified resource for host-pathogen interactions

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