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

By Suraj Peri, J. Navarro, Ramars Amanchy, Troels Kristiansen, Chandra Kiran Jonnalagadda, Vineeth Surendranath, Vidya Niranjan, B. Muthusamy, T. K. Gandhi, M. Grønborg and 42 more. Genome Research, 2003

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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.

Subfields: Genetics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/befc8b8f3865cfbb35634ea4db4aeca20a339d71

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Citations in the corpus

Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment (2019, background): “…al., 2014), ChEMBL (Gaulton et al., 2012), and PubChem (Wang et al., 2009)], target interaction databases [STRING (Szklarczyk et al., 2015), HPRD (Peri et al., 2003), MINT (Zanzoni et al., 2002), IntAct (Kerrien et al., 2012), Reactome (D’Eustachio, 2009), and HAPPI (Chen et al., 2009)], and…”
GeneTrail—advanced gene set enrichment analysis (2007, background): “The current version of BNþþ integrates for example the following biological data sources: RefSeq (12), KEGG (13), TRANSPATH (14), TRANSFAC (15), DIP (16), MINT (17), HPRD (18), IntAct (19).”
Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network (2010, methodology): “The protein–protein interaction (PPI) data were derived from Human Protein Reference Database (HPRD; Peri et al., 2003).”
Protein complex prediction via cost-based clustering (2004, methodology): “, 2002; Peri et al., 2003). Similarly as in Pržulj et al. (2004), RNSC identified Rib15, Rib7 as a functionally homogeneous cluster (riboflavin biosynthesis) with density 1.”
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. (2007, methodology): “Known protein–protein interactions are queried from the HPRD [24].”
Probabilistic model of the human protein-protein interaction network (2005, background): “The GSP interaction set was downloaded from the HPRD (http://www.hprd.org).”
Network-based methods for human disease gene prediction. (2011, neutral): “…by small-scale experiments, as was done in a large number of databases such as Human Protein Reference Database (HPRD), Molecular Interaction database (MINT), Biological General Repository for Interaction data sets (BioGRID), Biomolecular Interaction Network Database (BIND) and IntAct [18–22].”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, positive): “In addition, bioinformatic analyses have been performed, collecting information on human interactions from hypothesis-driven studies [ 30 ] or from studies identifying conserved orthologous interactions [23], which are referred to as “interologs” [27,42].”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, neutral): “HPRD [123] http://www.”
Online Predicted Human Interaction Database (2005, neutral): “Many databases are devoted to the human interactome, with a substantial number of them appearing in recent months (DIP, HPID, HPRD, MINT, PINdb (Han et al. , 2004; Luc and Tempst, 2004; Peri et al. , 2003; Xenarios et al. , 2000; Zanzoni et al. , 2002)).”
Identifying functional modules in protein–protein interaction networks: an integrated exact approach (2008, background): “Following Pounds and Morris (2003) we consider the distribution of the P-values as a mixture of a noise and a signal component.”
Interactome: gateway into systems biology. (2005, background): “Computational genomics utilizes information on individual protein interactions taken from publicly available databases such as BIND (71), MIPS (72) and HPRD (73,74), relies on annotations defined by Pfam (19), GO (20), and combines these data with sequence similarities within genomes and orthologies”