Protein-interaction-network-based pathway analysis (**PINBPA**) is a novel tool to analyze **GWAS** data in a network fashion. User can easily import GWAS data, draw Manhattan plots, define blocks, prioritize genes with random walk with restart, detect enriched sub-networks and test the significance of sub-networks via a user-friendly interface.
PINBPA has been implemented as Cytoscape app (3.0 and later versions) using Java. Additionally, R scripts are called via Rserve (http://rforge.net/Rserve/) inside Cytoscape for plotting.
PINBPA offers six features:
(1)Generating a gene-wise Manhattan plot of the GWAS;
(2) Sorting all genes by their genomic coordinates and defines association blocks at any user-defined threshold;
(3) Annotating the user-selected PPI network with imported gene-wise GWAS p-values;
(4) Generateing a sub-network of only significant genes (first-order networks) exceeding a user-defined threshold, and testing the statistical significance of the sub-networks using random permutations;
(5) Running gene prioritization using a random walk with restart algorithm;
(6) Detecting sub-networks enriched in significant genes using either unweighted or weighted z-scores.
PINBPA: Cytoscape app for network analysis of GWAS data, *Bioinformatics*, 2014.
**Updates in version 1.1.9**: Updated with importing VEGAS output file without SNP and SNP-pvalue columns, which were the last two columns in our default file.
**Updates in version 1.1.8**: Fixed a bug to plot histograms from the permutations of the first-order network.
**Updates in version 1.1.7**: (1) To print out the percentile of the first-order network in random permutation in command line, if the user starts Cytoscape by running cytoscape.bat in Windows or cytoscape.sh in Linux or Mac OS X; and (2) renamed "Network Permutation" panel as "First-order Network", renamed "Greedy Search" panel as "Module Search", and adjusted the order of panels.