Human Proteinpedia: A unified discovery resource for proteomics research

Kumaran Kandasamy, Shivakumar Keerthikumar, Renu Goel, Suresh Mathivanan, Nandini Patankar, Beema Shafreen, Santosh Renuse, Harsh Pawar, Y. L. Ramachandra, Pradip Kumar Acharya, Prathibha Ranganathan, Raghothama Chaerkady, T. S. Keshava Prasad, Akhilesh Pandey

Research output: Contribution to journalArticle

64 Scopus citations

Abstract

Sharing proteomic data with the biomedical community through a unified proteomic resource, especially in the context of individual proteins, is a challenging prospect. We have developed a community portal, designated as Human Proteinpedia (http://www.humanproteinpedia.org/), for sharing both unpublished and published human proteomic data through the use of a distributed annotation system designed specifically for this purpose. This system allows laboratories to contribute and maintain protein annotations, which are also mapped to the corresponding proteins through the Human Protein Reference Database (HPRD; http://www.hprd.org/). Thus, it is possible to visualize data pertaining to experimentally validated posttranslational modifications (PTMs), protein isoforms, protein-protein interactions (PPIs), tissue expression, expression in cell lines, subcellular localization and enzyme substrates in the context of individual proteins. With enthusiastic participation of the proteomics community, the past 15 months have witnessed data contributions from more than 75 labs around the world including 2710 distinct experiments, < 1.9 million peptides, < 4.8 million MS/MS spectra, 150 368 protein expression annotations, 17 410 PTMs, 34 624 PPIs and 2906 subcellular localization annotations. Human Proteinpedia should serve as an integrated platform to store, integrate and disseminate such proteomic data and is inching towards evolving into a unified human proteomics resource.

Original languageEnglish (US)
Pages (from-to)D773-D781
JournalNucleic acids research
Volume37
Issue numberSUPPL. 1
DOIs
StatePublished - 2009

ASJC Scopus subject areas

  • Genetics

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    Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Keshava Prasad, T. S., & Pandey, A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic acids research, 37(SUPPL. 1), D773-D781. https://doi.org/10.1093/nar/gkn701