Development of human protein reference database as an initial platform for approaching systems biology in humans - PubMed (original) (raw)

. 2003 Oct;13(10):2363-71.

doi: 10.1101/gr.1680803.

J Daniel Navarro, Ramars Amanchy, Troels Z Kristiansen, Chandra Kiran Jonnalagadda, Vineeth Surendranath, Vidya Niranjan, Babylakshmi Muthusamy, T K B Gandhi, Mads Gronborg, Nieves Ibarrola, Nandan Deshpande, K Shanker, H N Shivashankar, B P Rashmi, M A Ramya, Zhixing Zhao, K N Chandrika, N Padma, H C Harsha, A J Yatish, M P Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Shubha Suresh, Neelanjana Ghosh, R Saravana, Sreenath Chandran, Subhalakshmi Krishna, Mary Joy, Sanjeev K Anand, V Madavan, Ansamma Joseph, Guang W Wong, William P Schiemann, Stefan N Constantinescu, Lily Huang, Roya Khosravi-Far, Hanno Steen, Muneesh Tewari, Saghi Ghaffari, Gerard C Blobe, Chi V Dang, Joe G N Garcia, Jonathan Pevsner, Ole N Jensen, Peter Roepstorff, Krishna S Deshpande, Arul M Chinnaiyan, Ada Hamosh, Aravinda Chakravarti, Akhilesh Pandey

Affiliations

Development of human protein reference database as an initial platform for approaching systems biology in humans

Suraj Peri et al. Genome Res. 2003 Oct.

Abstract

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

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Figures

Figure 1

Figure 1

The query page of HPRD. A screenshotof HPRD query system shows differentfields by which a user can effectively search the database. The query system allows Boolean searches across the entire database. Pop-up lists that allow a user to choose the terms for querying are provided for most fields.

Figure 2

Figure 2

A screenshotshowing the molecule page of “Fyn” in HPRD. The molecule page shows a graphic representation of Fyn with its protein domains as polygons and sites of posttranslational modifications as vertical straightor wavy lines (colored symbols atthe end of lines representdifferent posttranslational modifications). Moving the cursor over the graph shows detailed domain names, range of amino acids, type of modification, and site of modification. The tabs guide the user to other annotated fields of the molecule. The summary tab shows a description of molecular weight, locus, subcellular localization, domain architecture details, and functions. For every molecule, the left panel shows links to query, browse, BLAST, and pathways pages. Most annotations are linked to corresponding PubMed articles that are accessible by clicking on the text.

Figure 3

Figure 3

Distribution of types of experiments used to derive protein-protein interactions in HPRD based on reading of the literature.

Figure 4

Figure 4

A distribution of the number of interaction partners per protein in HPRD. The histogram shows the distribution of proteins with zero to one, two, three, four, or five or more interaction partners out of a total of 10,534 interactions.

Figure 5

Figure 5

The EGF receptor signaling pathway generated by using the data contained in HPRD. The graph was drawn by using Pajek program and further manipulated manually (Batagelj and Mrvar 1998). The major signaling molecules involved in the EGF receptor pathway are labeled in red boxes. The interactors of the major proteins are shown as small circles. The graphs are generated in Scalable Vector Graphics (SVG), which allows the user to zoom in without any loss of resolution. Clicking any node links to the corresponding molecule page in HPRD.

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References

    1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410. - PubMed
    1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. - PMC - PubMed
    1. Bader, G.D. and Hogue, C.W. 2002. Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20: 991-997. - PubMed
    1. Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F., Pawson, T., and Hogue, C.W. 2001. BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res. 29: 242-245. - PMC - PubMed
    1. Batagelj, V. and Mrvar, A. 1998. Pajek: Program for large network analysis. Connections 21: 47-57.

WEB SITE REFERENCES

    1. http://www.hprd.org; Human Protein Reference Database.
    1. http://www.ibioinformatics.org; Institute of Bioinformatics home page.

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