Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

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.

Probabilistic model of the human protein-protein interaction network

“…Based on previous reports, we suspected that (i) model organism interactions may suggest interactions among orthologous human proteins 5,6 , (ii) similar gene expression profiles across a panel of human tissue samples may identify interacting protein products 7,8 , (iii) protein domain pairs enriched among known human protein-protein interactions may suggest novel interactions 9 , (iv) shared functional annotations from Gene Ontology 4 may suggest physical interactions, and (v) that combining evidence from independent data sources may strongly predict protein-protein interactions [10][11][12] . To test these hypotheses, we applied a naive Bayes classifier 7 , a method well-suited for integrating disparate data types.…”

“…A gold standard positive set (GSP) of 11,678 distinct protein-protein interactions among 5,505 proteins was queried from the Human Protein Reference Database (HPRD) 12 , a resource that contains known protein-protein interactions manually curated from the literature by expert biologists. A gold standard negative set (GSN) of 3,106,928 protein pairs was defined, in which one protein was assigned to the plasma membrane cellular component and the other to the nuclear cellular component by the Gene Ontology Consortium 4 .…”

StrokeBase: A Database of Cerebrovascular Disease-related Candidate Genes

“…A protein-protein network diagram that showed the integrated markers and their relationships was constructed in order to analyze the network characteristics and produce hub genes. It was found that the PPI network that was associated with cerebrovascular disease follows a power-law degree distribution, as other biological networks do (Peri et al, 2003). The PathwayStudio 5.0 program (Ariadne, Inc., MD, USA) was utilized to process the natural text mining of PubMed abstracts; the use of PathwayStudio resulted in a gene-disease association network.…”

Untitled

“…We obtained two human gene/protein networks, one from Human Protein Reference Database (HPRD) (Mishra et al 2006;Peri et al 2003;Prasad et al 2009) and another from MultiNet (Khurana et al 2013 Algorithm (van Dongen 2000). Clustering was done with the inflation parameter I ranging from 1.1 to 2.0 with a step of 0.1.…”