PINA v2.0: mining interactome modules

Abstract

The Protein Interaction Network Analysis (PINA) platform is a comprehensive web resource, which includes a database of unified protein–protein interaction data integrated from six manually curated public databases, and a set of built-in tools for network construction, filtering, analysis and visualization. The second version of PINA enhances its utility for studies of protein interactions at a network level, by including multiple collections of interaction modules identified by different clustering approaches from the whole network of protein interactions (‘interactome’) for six model organisms. All identified modules are fully annotated by enriched Gene Ontology terms, KEGG pathways, Pfam domains and the chemical and genetic perturbations collection from MSigDB. Moreover, a new tool is provided for module enrichment analysis in addition to simple query function. The interactome data are also available on the web site for further bioinformatics analysis. PINA is freely accessible at http://cbg.garvan.unsw.edu.au/pina/.

Phosphoproteomic Profiling Identifies Focal Adhesion Kinase as a Mediator of Docetaxel Resistance in Castrate-Resistant Prostate Cancer

“…The hypergeometric test was selected to test statistical enrichment of KEGG and Reactome pathways, and the P values were corrected for multiple comparisons (22). The protein-protein interactions among proteins of interest were retrieved from the Protein Interaction Network Analysis platform (23), and substrate-kinase relationships were downloaded from the PhosphoSitePlus database (24). Cytoscape (25) was used for visualization of networks.…”

Valorizing omics visualization for discovery

“…The Cytoscape App Store (http:// apps.cytoscape.org/) provides downloads of several plugins, such as CyLineUpi [5], PINA4MS [6], PTMOracle [42] that perform visualizations of omics data on network or pathway maps although most plugins do not permit the overlay of several different data types in one visualization. Furthermore, there are several web-based tools developed for the visualization of omics data on pathway maps.…”

Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study

“…PPIs were downloaded from the Protein Interaction Network Analysis version 2 (PINA v2.0) database, which collected and curated 108,477 PPI pairs from six manually curated public repositories (Cowley et al 2012). Only the experimentally validated PPIs were used.…”

“…We computed the reduction of gene coexpression in terms of "relative difference" between the Spearman's ρ and the SOPC, and then carefully utilized that in predicting miR-5p/-3p coregulated target genes. Next, we computed the gene expression correlation for each pair of interacting proteins in the curated human protein-protein interaction (PPI) network (Cowley et al 2012) to find a meaningful biological context for miR-5p/-3p coregulated genes.…”