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PINA4MS 2.0

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The Protein Interaction Network Analysis For Multiple Sets (PINA4MS) combines the curated protein-protein interactions from PINA and kinase-substrate relationships from PhosphoSitePlus to identify interactions between and within multiple groups of genes of interest. Tissue-specific protein expression data and RNA-seq data from the Human Protein Atlas (HPA) is aslo integrated in Release 2.0.

In Release 2.0, a number of new features were developed, including:

1. Integration of HPA expression data for normal and tumour tissues, with the node size proportional to the expression level;
2. Identification and retrieval of additional proteins that interact with the input proteins;
3. Highlight interactions based on HPA tissue-specific protein expression (antibody proteomics), mRNA expression (RNA-seq), or subcellular location (confocal immunofluorescence);
4. Highlight interactions for which the interacting partners have correlated expression pattern across the HPA profiled tissues or cell lines.

A number of advanced visualization features have been supported in all releases, including:

1. Customized node pie chart allowing users to easily identify common and distinct proteins in the input groups, as well as interactions between different groups.
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 3.1
• The latest version of PINA4MS can be directly downloaded within Cytoscape 3.1 (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 3.1 (or later), and click the menu "Apps -> App Manager". From the dialogue box, click the button "Install from File...".

User Guide

A detailed user guide with figures can be downloaded Here.

Previous releases

Release 1.1
Release 1.0