PINBPA

Protein-interaction-network-based Pathway Analysis
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. Reference: 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. Please check [http://www.pinbpa.com] for details.

1.1.9.Beta

Works with Cytoscape 3.0


1.1.8

Works with Cytoscape 3.0


1.1.7

Works with Cytoscape 3.0


1.1.6.Beta

Works with Cytoscape 3.0


1.1.5.Beta

Works with Cytoscape 3.0


1.1.4.Beta

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.1.9.Beta

Released 11 Jul 2016

Works with Cytoscape 3.0

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