Human Protein Reference Database: Difference between revisions

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{{Short description|Online database of proteins}}

{{primary sources|date=November 2008}}

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==Overview==

The HPRD is a result of an international collaborative effort between the [[Institute of Bioinformatics', Bangalore| Institute of Bioinformatics]] in Bangalore, India and the [[Akhilesh Pandey (scientist)| 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 Online Mendelian Inheritance in Man (OMIM) database. The National Center for Biotechnology Information provides link to HPRD through its human protein databases (e.g. Entrez Gene, RefSeq protein pertaining to genes and proteins.

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>{{cite journal | author = Gandhi T.K.B. | title = Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets | journal = Nature Genetics | volume = 38| issue = 3| pages = 285–293 | doi=10.1038/ng1747 | pmid=16501559 | date=March 2006| s2cid = 1446423 |display-authors=etal}}</ref>

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Highlights of HPRD as follows:

* 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>{{cite journal | author = Mathivanan S. | year = 2006| title = An evaluation of human protein–protein interaction data in the public ___domain | journal = BMC Bioinformatics | volume = 2006 | issue = 7| page = S19 | doi=10.1186/1471-2105-7-s5-s19|display-authors=etal | pmid=17254303 | pmc=1764475| doi-access = free}}</ref>

* More than 50% of molecules annotated in HPRD have at least one PPI and 10% have more than 10 PPIs.

* Experiments for PPIs are broadly grouped into three categories namely in vitro, in vivo and [[yeast two hybrid]] (Y2H). Sixty percent of PPIs annotated in HPRD are supported by a single experiment whereas 26% of them are found to have two of the three experimental methods annotated.

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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 |title=An evaluation of human protein-protein interaction data in the public ___domain |journal=[[BMC Bioinformatics]] |volume=7 Suppl 5 |pages=S19 |year=2006 |pmid=17254303 |pmc=1764475 |doi=10.1186/1471-2105-7-S5-S19 |name-list-style=vanc |author2=Periaswamy B |author3=Gandhi TK |display-authors=3 |last4=Kandasamy |first4=Kumaran |last5=Suresh |first5=Shubha |last6=Mohmood |first6=Riaz |last7=Ramachandra |first7=YL |last8=Pandey |first8=Akhilesh |issue=Suppl 5 |doi-access=free }}</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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==External links==

*http://www.humanproteinpedia.org {{Webarchive|url=https://web.archive.org/web/20070314135408/http://www.humanproteinpedia.org/ |date=2007-03-14 }}

*http://www.hprd.org {{Webarchive|url=https://web.archive.org/web/20060424071622/http://www.hprd.org/ |date=2006-04-24 }}

*http://www.hprd.org

[[Category:BiologicalProtein databases]]

[[Category:Online databases]]