Human Protein Reference Database: Difference between revisions

Revision as of 15:11, 4 March 2012

Revision as of 10:06, 10 September 2012

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{{primarysources|date=November 2008}}

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, 2363–71</ref>

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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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>Mathivanan, S. ''et al.'' An evaluation of human protein–protein interaction data in the public ___domain. ''BMC Bioinformatics''. 2006. 7, S19</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.

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

• * HPRD contains 18,000 manually curated PTMs data belonging to 26 different types. [[Phosphorylation]] is the leading type of modification of protein contributing to 63% of PTM data annotated in HPRD. [[Glycosylation]], [[proteolytic cleavage]] and [[disulfide bridge]] events are the next leading contributors of PTM data.

• * HPRD data is available for download in tab delimited and [[XML]] file formats.<ref>Mishra, G. ''et al.'' Human protein reference database—2006 update. ''Nucleic Acids Research''. 2006. 34, 411–414</ref>

• 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.

• HPRD contains 18,000 manually curated PTMs data belonging to 26 different types. [[Phosphorylation]] is the leading type of modification of protein contributing to 63% of PTM data annotated in HPRD. [[Glycosylation]], [[proteolytic cleavage]] and [[disulfide bridge]] events are the next leading contributors of PTM data.

• HPRD data is available for download in tab delimited and [[XML]] file formats.<ref>Mishra, G. ''et al.'' Human protein reference database—2006 update. ''Nucleic Acids Research''. 2006. 34, 411–414</ref>

HPRD also integrates data from [[Human Proteinpedia]], a community portal for integrating human protein data. The data from HPRD can be freely accessed and used by academic users while commercial entities are required to obtain a license for use. Human Proteinpedia<ref>Mathivanan, S. ''et al.'' Human Proteinpedia enables sharing of human protein data. ''Nature Biotechnology''. 2008. 26, 164–167</ref> content is freely available for anyone to download and use.