Issue 2, 2012
From the journal:

Molecular BioSystems

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

Renu Goel,*ab   H. C. Harsha,a   Akhilesh Pandeycde  and  T. S. Keshava Prasad*af  

* Corresponding authors

a Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
E-mail: renu@ibioinformatics.org, keshav@ibioinformatics.org

b Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India

c McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland

d Departments of Biological Chemistry, Baltimore, Maryland

e Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland

f Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Pondicherry, India

Abstract

Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein–protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein–protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95 016 phosphosites mapped on to 13 041 proteins. Additionally, enzyme–substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.

Graphical abstract: Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

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Article information

DOI
https://doi.org/10.1039/C1MB05340J
Article type
Review Article
Submitted
19 Aug 2011
Accepted
06 Oct 2011
First published
08 Dec 2011

Mol. BioSyst., 2012,8, 453-463

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Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

R. Goel, H. C. Harsha, A. Pandey and T. S. K. Prasad, Mol. BioSyst., 2012, 8, 453 DOI: 10.1039/C1MB05340J

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