Human protein reference database as a discovery resource for proteomics

Abstract

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.

Predicting Subcellular Localization via Protein Motif Co-Occurrence

“…Also, Pr[M] is the prior probability of a protein-containing motif set M regardless of the localization of the proteins containing M. This prior probability is estimated by determining the presence of InterPro motifs in all 9793 human proteins from SWISS-PROT release 41.25. Lastly, Pr[C] is the prior probability of a protein localizing to compartment C. These compartment priors were initially evaluated by averaging the number of human proteins annotated with localization information in three public databases: SWISS-PROT (Boeckmann et al 2003), Human Protein Reference Database (www.hprd.org/; Peri et al 2004), and LIFEdb (Simpson et al 2000). The compartment priors were subsequently modified; this modification is described in "Compartment Prior Optimization.…”

Understanding biological functions through molecular networks

“…For now, such information covers only a tiny fraction of the full network and is biased towards certain biological functions. For example, protein interactions in the literature curated by HPRD (Human Protein Reference Database) [14] cover only 20 000 interactions out of a conservative estimate of 150 000 interactions and are strongly biased for cancer-related processes (Supplementary information, table S1). Large-scale experiments and data mining are obviously more effective for mapping genetic networks [15].…”

Discovering Regulated Networks During Hiv-1 Latency and Reactivation

“…Human -human protein interaction data was culled from HPRD [15] (June 2005 download) and protein fragments were BLAST matched to Entrez Gene and unigene identifiers. HIVhuman interactions were taken from the HIV-1, human interaction database [16].…”

“…Recently, the curation efforts of the Human Protein Reference Database (HPRD) have produced high confidence protein-protein interaction networks derived from literature on a scale such that systems biology based modeling is possible [15]. Additionally, the NCBI has produced a HIV-1-human protein interaction database, providing a summary of known interactions of HIV-1 proteins with those of the host cell [18].…”

“…However, manually curated protein interaction data is preferable to automated prediction of interactions through natural language processing. The Human Protein Reference Database (HPRD) includes information on protein-protein interactions, post-translational modifications, enzymesubstrate relationships and disease association of human genes which was derived manually by a critical reading of the published literature by expert biologists [15]. Another manually curated database, the HIV-1, human interaction database, provides protein-protein interaction data among 7 of the 9 (excluding env and nef) HIV-1 genes and human host cell genes [16].…”