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

Suraj Peri, 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. HarshaA. 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, Akhiley Pandey

Research output: Contribution to journalArticle

758 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2363-2371
Number of pages9
JournalGenome Research
Volume13
Issue number10
DOIs
StatePublished - Oct 1 2003

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Protein Databases
Systems Biology
Human Development
Proteins
Cataloging
Databases
Post Translational Protein Processing
Computational Biology
Proteomics
Technology
Health
Enzymes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., ... Pandey, A. (2003). Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research, 13(10), 2363-2371. https://doi.org/10.1101/gr.1680803

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

In: Genome Research, Vol. 13, No. 10, 01.10.2003, p. 2363-2371.

Research output: Contribution to journalArticle

Peri, S, Navarro, JD, Amanchy, R, Kristiansen, TZ, Jonnalagadda, CK, Surendranath, V, Niranjan, V, Muthusamy, B, Gandhi, TKB, Gronborg, M, Ibarrola, N, Deshpande, N, Shanker, K, Shivashankar, HN, Rashmi, BP, Ramya, MA, Zhao, Z, Chandrika, KN, Padma, N, Harsha, HC, Yatish, AJ, Kavitha, MP, Menezes, M, Choudhury, DR, Suresh, S, Ghosh, N, Saravana, R, Chandran, S, Krishna, S, Joy, M, Anand, SK, Madavan, V, Joseph, A, Wong, GW, Schiemann, WP, Constantinescu, SN, Huang, L, Khosravi-Far, R, Steen, H, Tewari, M, Ghaffari, S, Blobe, GC, Dang, CV, Garcia, JGN, Pevsner, J, Jensen, ON, Roepstorff, P, Deshpande, KS, Chinnaiyan, AM, Hamosh, A, Chakravarti, A & Pandey, A 2003, 'Development of human protein reference database as an initial platform for approaching systems biology in humans', Genome Research, vol. 13, no. 10, pp. 2363-2371. https://doi.org/10.1101/gr.1680803
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research. 2003 Oct 1;13(10):2363-2371. https://doi.org/10.1101/gr.1680803
Peri, Suraj ; Navarro, J. Daniel ; Amanchy, Ramars ; Kristiansen, Troels Z. ; Jonnalagadda, Chandra Kiran ; Surendranath, Vineeth ; Niranjan, Vidya ; Muthusamy, Babylakshmi ; Gandhi, T. K.B. ; Gronborg, Mads ; Ibarrola, Nieves ; Deshpande, Nandan ; Shanker, K. ; Shivashankar, H. N. ; Rashmi, B. P. ; Ramya, M. A. ; Zhao, Zhixing ; Chandrika, K. N. ; Padma, N. ; Harsha, H. C. ; Yatish, A. J. ; Kavitha, M. P. ; Menezes, Minal ; Choudhury, Dipanwita Roy ; Suresh, Shubha ; Ghosh, Neelanjana ; Saravana, R. ; Chandran, Sreenath ; Krishna, Subhalakshmi ; Joy, Mary ; Anand, Sanjeev K. ; Madavan, V. ; Joseph, Ansamma ; Wong, Guang W. ; Schiemann, William P. ; Constantinescu, Stefan N. ; Huang, Lily ; Khosravi-Far, Roya ; Steen, Hanno ; Tewari, Muneesh ; Ghaffari, Saghi ; Blobe, Gerard C. ; Dang, Chi V. ; Garcia, Joe G.N. ; Pevsner, Jonathan ; Jensen, Ole N. ; Roepstorff, Peter ; Deshpande, Krishna S. ; Chinnaiyan, Arul M. ; Hamosh, Ada ; Chakravarti, Aravinda ; Pandey, Akhiley. / Development of human protein reference database as an initial platform for approaching systems biology in humans. In: Genome Research. 2003 ; Vol. 13, No. 10. pp. 2363-2371.
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