Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (356K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Peri, S.
Right arrow Articles by Pandey, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Peri, S.
Right arrow Articles by Pandey, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2004, Vol. 32, Database issue D497-D501
© 2004 Oxford University Press

Human protein reference database as a discovery resource for proteomics

Suraj Peri1,2, J. Daniel Navarro1,3, Troels Z. Kristiansen1,2, Ramars Amanchy1, Vineeth Surendranath4, Babylakshmi Muthusamy4, T. K. B. Gandhi4, K. N. Chandrika4, Nandan Deshpande4, Shubha Suresh4, B. P. Rashmi4, K. Shanker4, N. Padma4, Vidya Niranjan4, H. C. Harsha4, Naveen Talreja4, B. M. Vrushabendra4, M. A. Ramya4, A. J. Yatish4, Mary Joy4, H. N. Shivashankar4, M. P. Kavitha4, Minal Menezes4, Dipanwita Roy Choudhury4, Neelanjana Ghosh4, R. Saravana4, Sreenath Chandran4, Sujatha Mohan4, Chandra Kiran Jonnalagadda1,4, C. K. Prasad4, Chandan Kumar-Sinha4, Krishna S. Deshpande4 and Akhilesh Pandey*,1

1 McKusick–Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21287, USA, 2 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark, 3 Departamento de Automática y Computación, Área de Ciencias de la Computación e Inteligencia Artificial, Universidad Pública de Navarra, 31006 Pamplona, Spain and 4 Institute of Bioinformatics, Discoverer 7th Floor, International Technology Park Ltd, Bangalore 560 066, India

*To whom correspondence should be addressed. Tel: +1 410 502 6662; Fax: +1 410 502 7543; Email: pandey{at}jhmi.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein–protein interactions, post-translational modifications, enzyme–substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
C. M. Song, S. J. Lim, and J. C. Tong
Recent advances in computer-aided drug design
Brief Bioinform, September 1, 2009; 10(5): 579 - 591.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Chen, E. E. Bardes, B. J. Aronow, and A. G. Jegga
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W305 - W311.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, and R. Nussinov
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
Brief Bioinform, May 1, 2009; 10(3): 217 - 232.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Georgii, S. Dietmann, T. Uno, P. Pagel, and K. Tsuda
Enumeration of condition-dependent dense modules in protein interaction networks
Bioinformatics, April 1, 2009; 25(7): 933 - 940.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Kandasamy, S. Keerthikumar, R. Goel, S. Mathivanan, N. Patankar, B. Shafreen, S. Renuse, H. Pawar, Y. L. Ramachandra, P. K. Acharya, et al.
Human Proteinpedia: a unified discovery resource for proteomics research
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D773 - D781.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, et al.
Human Protein Reference Database--2009 update
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D767 - D772.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc AHome page
M. Hofmann-Apitius, J. Fluck, L. Furlong, O. Fornes, C. Kolarik, S. Hanser, M. Boeker, S. Schulz, F. Sanz, R. Klinger, et al.
Knowledge environments representing molecular entities for the virtual physiological human
Phil Trans R Soc A, September 13, 2008; 366(1878): 3091 - 3110.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Park, B.-C. Kim, S.-W. Cho, S.-J. Park, J.-S. Choi, S. I. Kim, J. Bhak, and S. Lee
MassNet: a functional annotation service for protein mass spectrometry data
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W491 - W495.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Li, P. Agarwal, and D. Rajagopalan
A global pathway crosstalk network
Bioinformatics, June 15, 2008; 24(12): 1442 - 1447.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
D. Li, W. Liu, Z. Liu, J. Wang, Q. Liu, Y. Zhu, and F. He
PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources
Mol. Cell. Proteomics, June 1, 2008; 7(6): 1043 - 1052.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
E.-M. Duerr, Y. Mizukami, A. Ng, R. J Xavier, H. Kikuchi, V. Deshpande, A. L Warshaw, J. Glickman, M. H Kulke, and D. C Chung
Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis
Endocr. Relat. Cancer, March 1, 2008; 15(1): 243 - 256.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. Yao and A. Rzhetsky
Quantitative systems-level determinants of human genes targeted by successful drugs
Genome Res., February 1, 2008; 18(2): 206 - 213.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Z. Guo, Y. Li, X. Gong, C. Yao, W. Ma, D. Wang, Y. Li, J. Zhu, M. Zhang, D. Yang, et al.
Edge-based scoring and searching method for identifying condition-responsive protein protein interaction sub-network
Bioinformatics, August 15, 2007; 23(16): 2121 - 2128.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
N. G. Faux, G. A. Huttley, K. Mahmood, G. I. Webb, M. Garcia de la Banda, and J. C. Whisstock
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
Genome Res., July 1, 2007; 17(7): 1118 - 1127.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. J. Gaulton, K. L. Mohlke, and T. J. Vision
A computational system to select candidate genes for complex human traits
Bioinformatics, May 1, 2007; 23(9): 1132 - 1140.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
S. Savas, I. W. Taylor, J. L. Wrana, and H. Ozcelik
Functional nonsynonymous single nucleotide polymorphisms from the TGF-{beta} protein interaction network
Physiol Genomics, April 24, 2007; 29(2): 109 - 117.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. Fundel, R. Kuffner, and R. Zimmer
RelEx--Relation extraction using dependency parse trees
Bioinformatics, February 1, 2007; 23(3): 365 - 371.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Villen, S. A. Beausoleil, S. A. Gerber, and S. P. Gygi
Large-scale phosphorylation analysis of mouse liver
PNAS, January 30, 2007; 104(5): 1488 - 1493.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. Przulj
Biological network comparison using graphlet degree distribution
Bioinformatics, January 15, 2007; 23(2): e177 - e183.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil
Resources for integrative systems biology: from data through databases to networks and dynamic system models
Brief Bioinform, December 1, 2006; 7(4): 318 - 330.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Letunic, R. R. Copley, B. Pils, S. Pinkert, J. Schultz, and P. Bork
SMART 5: domains in the context of genomes and networks
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D257 - D260.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, S. Suresh, P. Bala, K. Shivakumar, N. Anuradha, R. Reddy, T. M. Raghavan, et al.
Human protein reference database--2006 update
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D411 - D414.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
U. Guldener, M. Munsterkotter, M. Oesterheld, P. Pagel, A. Ruepp, H.-W. Mewes, and V. Stumpflen
MPact: the MIPS protein interaction resource on yeast
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D436 - D441.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D527 - D534.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
R. R. Miles, D. K. Crockett, M. S. Lim, and K. S. J. Elenitoba-Johnson
Analysis of BCL6-interacting Proteins by Tandem Mass Spectrometry
Mol. Cell. Proteomics, December 1, 2005; 4(12): 1898 - 1909.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Espadaler, O. Romero-Isart, R. M. Jackson, and B. Oliva
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
Bioinformatics, August 15, 2005; 21(16): 3360 - 3368.
[Abstract] [Full Text] [PDF]

Home page
 J Mol EndocrinolHome page
A. Droit, G. G Poirier, and J. M Hunter
Experimental and bioinformatic approaches for interrogating protein-protein interactions to determine protein function
J. Mol. Endocrinol., April 1, 2005; 34(2): 263 - 280.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, L. Matthews, et al.
Reactome: a knowledgebase of biological pathways
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D428 - D432.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. J. Smink, E. M. Helton, B. C. Healy, C. C. Cavnor, A. C. Lam, D. Flamez, O. S. Burren, Y. Wang, G. E. Dolman, D. B. Burdick, et al.
T1DBase, a community web-based resource for type 1 diabetes research
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D544 - D549.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. S. Scott, D. Y. Thomas, and M. T. Hallett
Predicting Subcellular Localization via Protein Motif Co-Occurrence
Genome Res., October 1, 2004; 14(10a): 1957 - 1966.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.