PINA4MS

Combining tissue-specific protein expression and interaction data to identify genes of functional- and disease-relevance
The <b>P</b>rotein <b>I</b>nteraction <b>N</b>etwork <b>A</b>nalysis For <b>M</b>ultiple <b>S</b>ets (PINA4MS) combines the curated protein-protein interactions from [PINA](http://cbg.garvan.unsw.edu.au/pina/) and kinase-substrate relationships from [http://www.phosphosite.org/ 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](http://www.proteinatlas.org/) (HPA) is also integrated in Release 2.0.<br/> In Release 2.0, a number of new features were developed, including: <ol><li> Integration of HPA expression data for normal and tumour tissues, with the node size proportional to the expression level; </li><li> Identification and retrieval of additional proteins that interact with the input proteins; </li><li> Highlight interactions based on HPA tissue-specific protein expression (antibody proteomics), mRNA expression (RNA-seq), or subcellular location (confocal immunofluorescence); </li><li> Highlight interactions for which the interacting partners have correlated expression pattern across the HPA profiled tissues or cell lines. </li> </ol> <br/> A number of advanced visualization features have been supported in all releases, including: <ol><li><b>Customized node pie chart</b> allowing users to easily identify common and distinct proteins in the input groups, as well as interactions between different groups. </li><li>A <b>clickable Venn diagram</b> is provided on the side panel to support quick selection and highlight of exclusive set(s) of proteins in the network. A <b>clickable summary table </b> is shown at the bottom panel to indicate the number of interactions between the exclusive Venn sets ;</li><li>A customized layout algorithm, <b>Venn-Galaxy</b> layout, is implemented to provide an elaborate view on the localization of the protein sets and highlight the interface and connections in between.</li></ol> Click the link to see the User Guide for [PINA4MS 2.0](http://cbg.garvan.unsw.edu.au/pina/download/PINA4MS-UserGuide_2.0.pdf) or [PINA4MS 1.1](http://cbg.garvan.unsw.edu.au/pina/download/PINA4MS-UserGuide_1.1.pdf). Click the link to visit the [Home Page](http://cbg.garvan.unsw.edu.au/pina/interactome.pina4ms.do).

2.0.1

Works with Cytoscape 3.1

Release Notes

Fixed a bug, which makes PINA4MS fail to initialize on Mac OS X Yosemite.

2.0

Works with Cytoscape 3.1

Release Notes

Added support for integration of the tissue-specific expression data from the Human Protein Atlas (HPA).

1.1

Works with Cytoscape 3.0


1.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 2.0.1

Released 8 Jun 2015

Works with Cytoscape 3.1

Download Stats Click here

CYTOSCAPE 2

Version 1.1

Released 19 May 2014

Works with Cytoscape 2.8

Download Stats Click here