Human Protein Reference Database: Difference between revisions

Revision as of 23:11, 30 November 2008

Revision as of 11:57, 19 May 2009

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{{primarysources|date=November 2008}}

[[Image:HPRD.JPG|thumb|right|300 px|The HPRD provides a comprehensive link to any queried protein]]

The '''Human Protein Reference Database'''(HPRD) is a protein database accessible through the internet.<ref>Peri, S. ''et al.'' Development of human protein reference database as an initial platform for approaching systems biology in humans. ''Genome Research''. 2003. 13, 2363-2371</ref> <br />

The HPRD is a result of an international collaborative effort between the [http://www.ibioinformatics.org/ Institute of Bioinformatics] in Bangalore, India and the [http://pandeylab.igm.jhmi.edu/ Pandey lab] at [[Johns Hopkins University]] in Baltimore, USA. HPRD contains manually curated scientific information pertaining to the biology of most human proteins. Information regarding proteins involved in human diseases is annotated and linked to [http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim Online Mendelian Inhertance in Man] (OMIM) database. The [http://www.ncbi.nlm.nih.gov/ National Center for Biotechnology Information] provides link to HPRD through its human protein databases (e.g. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Entrez Gene], [http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq protein]) pertaining to genes and proteins.

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This resource depicts information on human protein functions including [[protein-protein interactions]], [[post-translational modifications]], enzyme-substrate relationships and [[disease]] associations. Protein annotation information that is catalogued was derived through manual curation using published literature by expert biologists and through bioinformatics analyses of the protein sequence. The protein-protein interaction and subcellular localization data from HPRD have been used to develop a human protein interaction network.<ref>Gandhi, T.K.B. ''et al.'' Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. ''Nature Genetics''. 2006. 3, 285-293</ref>

Highlights of HPRD as follows:<br />

• From 10,000 protein-protein interactions (PPIs) annotated for 3,000 proteins in 2003, HPRD has grown to over 36,500 unique PPIs annotated for 25,000 proteins including 6,360 isoforms by the end of 2007.<ref>Mathivanan, S. ''et al.'' An evaluation of human protein-protein interaction data in the public ___domain. ''BMC Bioinformatics''. 2006. 7, S19</ref>

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== Comparison of protein data ==

There are other databases that deal with human proteome (e.g. BioGRID, BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome). Each database has its own style of presenting the data. It is a difficult task for most investigators to compare the voluminous data from these databases in order to conclude strengths and weaknesses of each database. Mathivanan and colleagues <ref name="pmid17254303">{{cite journal |author=Mathivanan S, Periaswamy B, Gandhi TK, ''et al.'' |title=An evaluation of human protein-protein interaction data in the public ___domain |journal=[[BMC Bioinformatics]] |volume=7 Suppl 5 |issue= |pages=S19 |year=2006 |pmid=17254303 |pmc=1764475 |doi=10.1186/1471-2105-7-S5-S19 |url=http://www.biomedcentral.com/1471-2105/7%20Suppl%205/S19}}</ref> tried to address this issue while analyzing protein data by asking various questions. This analysis will help biologists to choose among these databases based on their needs.

== References ==

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*http://www.humanproteinpedia.org

*http://www.hprd.org

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[[Category:Bioinformatics]]