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. 2013 Mar:Chapter 1:1.21.1-1.21.15.
doi: 10.1002/0471250953.bi0121s41.

Access guide to human proteinpedia

Babylakshmi Muthusamy  1   2 , Joji Kurian Thomas  1   3 , T S Keshava Prasad  1   2   3 , Akhilesh Pandey  1   4
Affiliations

Access guide to human proteinpedia

Babylakshmi Muthusamy et al. Curr Protoc Bioinformatics. 2013 Mar.

Abstract

Human Proteinpedia (http://www.humanproteinpedia.org) is a publicly available proteome repository for sharing human protein data derived from multiple experimental platforms. It incorporates diverse features of the human proteome including protein-protein interactions, enzyme-substrate relationships, PTMs, subcellular localization, and expression of proteins in various human tissues and cell lines in diverse biological conditions including diseases. Through a publicly distributed annotation system developed especially for proteomic data, investigators across the globe can upload, view, and edit proteomic data even before they are published. Inclusion of information on investigators and laboratories that generated the data, as well as visualization of tandem mass spectra, stained tissue sections, protein/peptide microarrays, fluorescent micrographs, and western blots, ensures quality of proteomic data assimilated in Human Proteinpedia. Many of the protein annotations submitted to Human Proteinpedia have also been made available to the scientific community through Human Protein Reference Database (http://www.hprd.org), another resource developed by our group. In this protocol, we describe how to submit, edit, and retrieve proteomic data in Human Proteinpedia.

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Figures

Figure 1
Figure 1
The Human Proteinpedia query page. It provides options to search by gene symbol, protein name, external database accession number, tissue types, types of PTM and subcellular localization. It can also be queried by types of mass spectrometer or various experimental platforms.
Figure 2
Figure 2
Query results of tissue expression (e.g., brain). The table displays the types of experiments carried out to check expression of proteins in brain. It also provides the number of datasets fetched.
Figure 3
Figure 3
Targeted protein annotation page for PTMs.
Figure 4
Figure 4
Integration of Human Proteinpedia data into HPRD. It describes the incorporation Human Proteinpedia data for the molecule ‘Vimentin’. Along with the normal tissue expression, Human Proteinpedia data provides cancer and cell line expression also. All the expression data displayed in HPRD are hyperlinked to the dataset description page of Human Proteinpedia.
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References

    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. 2000;25:25–29. - PMC - PubMed
    1. Garavelli JS. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics. 2004;4:1527–1533. - PubMed
    1. Hamacher M, Klose J, Rossier J, Marcus K, Meyer HE. “Does understanding the brain need proteomics and does understanding proteomics need brains?”--Second HUPO HBPP Workshop hosted in Paris. Proteomics. 2004;4:1932–1934. - PubMed
    1. He F. Human liver proteome project: plan, progress, and perspectives. Molecular & cellular proteomics: MCP. 2005;4:1841–1848. - PubMed
    1. Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A. Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic acids research. 2009;37:D773–781. Update of Mathivanan et al., 2008 for the detailed explanation on various feature annotated in Human Proteinpedia and the potential uses of Human Proteinpedia data. - PMC - PubMed

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