Protein Interaction Network Analysis (PINA)

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract The Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management.

It integrates protein-protein interaction data from six (6) public curated databases (see below...) and builds a complete, non-redundant protein interaction dataset for six (6) model organisms (see below...).

Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network.

At the same time, PINA allows users to either edit the network generated from the public data, or combine these with uploaded private data to build more complete protein-protein interaction (PPI) networks.

The six (6) public curated databases are -- Molecular INTeraction database (MINT), IntAct (protein interaction data), Database of Interacting Proteins (DIP), Biological General Repository for Interaction Datasets (BioGRID);

Human Protein Reference Database (HPRD), and the Munich Information Center for Protein Sequences (MIPS)/MPact - MPact provides a common access point to interaction resources at MIPS.

The six (6) model organisms are -- Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, and Rattus norvegicus.

PINA features/capabilities:

1) Network Construction: Generate PPI networks from flexible query options --

Network construction generates the protein-protein interaction network from a) a single protein, b) a list of proteins, c) a list of protein pairs or d) two lists of proteins.

For example, input a list of up-regulated genes and a list of down-regulated genes from a microarray experiment.

2) Network Filter: Get a more credible network by different criteria --

The Network filter selects interactions from an existing network by specific criteria including a) detection method, b) interaction type, c) reference publication, d) user comment and e) semantic similarity of Gene Ontology (GO) terms.

The Network Filter (Annotation) selects interactions from the existing network by the following criteria:

3) Network Analysis: Gain the insight of the network --

Network analysis includes a) enriched GO term identification, b) topology feature calculation, c) identification of topologically important proteins in the interaction network, and d) identification of common interacting proteins.

4) Network Visualization: an interactive environment to view and edit a network --

Network visualization - provides an interactive tool to view, edit and analyze an interaction network. It can be launched in the query result page, “My networks” or “Shared networks”.

5) Network Download --

An interaction network can be downloaded to a local disk in the GraphML format, MITAB format or PINA tab-delimited format.

GraphML - GraphML is a XML format for graph representation. Node elements describe gene name, protein name, UniProt AC, GO terms of proteins; edge elements describe the interaction of proteins.

6) User space -- allows users to upload/edit interaction networks and to save your data on the server with account protection. The saved networks can be used as input to the analysis tools.

7) User community -- allows registered users (registration is free...) to write comments on interactions and share comments/networks with other users in PINA.

8) Data Integration: Non-redundant and more complete --

System Requirements

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Manufacturer Web Site PINA

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G6G Abstract Number 20706

G6G Manufacturer Number 104278