Human Protein Reference Database and Human Proteinpedia as Discovery Resources for Molecular Biotechnology

Abstract

In the recent years, research in molecular biotechnology has transformed from being small scale studies targeted at a single or a small set of molecule(s) into a combination of high throughput discovery platforms and extensive validations. Such a discovery platform provided an unbiased approach which resulted in the identification of several novel genetic and protein biomarkers. High throughput nature of these investigations coupled with higher sensitivity and specificity of Next Generation technologies provided qualitatively and quantitatively richer biological data. These developments have also revolutionized biological research and speed of data generation. However, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Data resources became necessary to assimilate, store and disseminate information that could allow future discoveries. We have developed two resources--Human Protein Reference Database (HPRD) and Human Proteinpedia, which integrate knowledge relevant to human proteins. A number of protein features including protein-protein interactions, post-translational modifications, subcellular localization, and tissue expression, which have been studied using different strategies were incorporated in these databases. Human Proteinpedia also provides a portal for community participation to annotate and share proteomic data and uses HPRD as the scaffold for data processing. Proteomic investigators can even share unpublished data in Human Proteinpedia, which provides a meaningful platform for data sharing. As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, molecular biology, cloning, and classical genetics in understanding the relationships among multiple facets of biological systems.

Dysregulation of splicing proteins in head and neck squamous cell carcinoma

“…The classifications were based on annotations in HPRD. 16,17 Our analysis revealed that 21% of the proteins were involved in regulation of nucleic acid metabolism; 18% in signal transduction, 15% in cell communication and 11% in cellular growth and maintenance. Classification of the proteins based on subcellular localization revealed 40% of the hyperphosphorylated proteins localized to the nucleus and 25% localized to the cytoplasm.…”

“…16,50 Pathway analysis was done using GeneSpring GX software (version 12.6.1). Using Pathway Architect module of GeneSpring GX, the proteins that were found to be overexpressed and hyperphosphorylated in at least four cell lines with a fold change of 1.5 was included for pathway analysis.…”

Shortest Path Analyses in the Protein-Protein Interaction Network of NGAL (Neutrophil Gelatinase-associated Lipocalin) Overexpression in Esophageal Squamous Cell Carcinoma

“…The newest versions of human protein-protein interaction dataset were available from HPRD, BioGRID and IntAct, respectively (Goel et al, 2011;Kerrien et al, 2012;Chatr-Aryamontri et al, 2013). These interactions are derived from literatures of experimentally validation and reliable for widely application in disease researches combined with human PPI network.…”

The Prediction and Analysis of Inter- and Intra-Species Protein-Protein Interaction

“…Interacting proteins have been observed to have topologically similar phylogenetic trees for the corresponding protein families, presumably due to the co-evolution of cooperating proteins (Fryxell, 1996;Goh et al, 2000;Pages et al, 1997). Based on the above observation, the phylogenetic similarity method was proposed.…”