Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis - PubMed
Review
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis
Renu Goel et al. Mol Biosyst. 2012 Feb.
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.
Figures
The molecule page for insulin receptor in Human Protein Reference Database is shown. Phosphorylation data is annotated through BioBuilder tool which is used to store and manage complex protein data. Each phosphorylation site is hyperlinked to the corresponding research articles that describes it. Wherever known, the upstream enzyme that phosphorylates a given site is also annotated.
A) Distribution of phosphorylation data in HPRD derived from in vivo and in vitro experiments B) Fraction of phosphosites in HPRD with an annotated upstream enzyme; C) Exponential increase of HPRD phosphorylation data over the last four releases; D) Distribution of protein groups based on number of phosphoserine, phosphothreonine and phosphotyrosine sites they harbor.
Microtubule associated protein 4 molecule page is shown in HPRD with links to Human Proteinpedia. PTMs page displays phosphorylation sites from HPRD and Human Proteinpedia. The upper right panel shows description of the peptide score, experimental description, peptide identification data, precursor mass, charge state, sequence identifier, algorithm, MS/MS spectrum, ionization method, fragmentation method and mass tolerance used for database searching. The hyperlink to MS/MS spectrum is given in lower right panel that helps users to inspect the spectrum manually.
The screenshots show PhosphoMotif Finder software that can be accessed through HPRD. PhosphoMotif Finder output for VEGF receptor 3 sequence query is shown.
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