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PINA4MS 1.1

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The Protein Interaction Network Analysis For Multiple Sets (PINA4MS) is a tool to identify and visualize intra- and inter-list biological interactions for multiple (up to four) lists of genes .

PINA4MS combines the curated protein-protein interactions from PINA and kinase-substrate relationships from PhosphoSitePlus to identify interactions between and within multiple lists of genes of interest. A number of unique features have also been developed to facilitate the analysis including:

1. Customized node pie chart allowing users to easily identify common and distinct proteins in the input sets, as well as interactions between different sets;
2. A clickable Venn diagram is provided on the side panel to support quick selection and highlight of exclusive set(s) of proteins in the network. A clickable summary table is shown at the bottom panel to indicate the number of interactions between the exclusive Venn sets ;
3. A customized layout algorithm, Venn-Galaxy layout, is implemented to provide an elaborate view on the localization of the protein sets and highlight the interface and connections in between.

Installation

There are 2 ways to get and install PINA4MS. The first way is to download it within Cytoscape, which will be followed by automatic installation. The other way is to manually download it form the links provided below, then install it through Cytoscape. Detailed instructions are listed below.

Cytoscape 3
• The latest version of PINA4MS can be directly downloaded within Cytoscape 3.0 (or later), by clicking the menu "Apps -> App Manager", and then searching with "PINA4MS" in the Install Apps section .
• Manual way: Download the latest PINA4MS, then launch Cytoscape 3.0 (or later), and click the menu "Apps -> App Manager". From the dialogue box, click the button "Install from File...".

Cytoscape 2
• You can download the latest PINA4MS version directly within Cytoscape 2.8 (or later), by clicking the menu "Plugins -> Manage Plugins" and then searching with "PINA4MS".
• Manual way: Download the latest PINA4MS, then launch Cytoscape 2.8 (or later), and click the menu "Plugins -> Install Plugin From File".

User Guide

A detailed user guide with figures can be downloaded Here.