PINA2

Introduction

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 public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network.

New Check PINA4MS 2.0 for a new way to construct and visualize interaction networks, seamlessly integrated with tissue-specific protein interaction data.

Usage

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

Interactome modules provide multiple collections of network modules identified from Interactomes by applying several clustering algorithms with different parameter settings. The identified modules have been compressively annotated with known knowledge from Gene Ontology, KEGG pathways, PFAM domains, and MeSigDB. User can either simply search modules or identify enriched modules from the list of query proteins,

Network filter selects interactions from the existing network by the specific criteria including detection method, interaction type, reference publication, user comment and semantic similarity of GO terms.

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

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

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

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

Interactome modules provides multiple collections of fully annotated modules identified from 6 PINA Interactomes. A new tool is also provided to identify enriched modules from users' query proteins.

Citing

Cowley, M.J., Pinese, M., Kassahn, K.S., Waddell, N., Pearson, J.V., Grimmond, S.M., Biankin, A.V., Hautaniemi, S. and Wu, J. (2012) PINA v2.0: mining interactome modules. Nucleic Acids Res, 40, D862-865. [Full text]

Wu, J., Vallenius, T., Ovaska, K., Westermarck, J., Makela, T.P. and Hautaniemi, S. (2009) Integrated network analysis platform for protein-protein interactions, Nature methods, 6, 75-77. [Abstract]

Acknowledgements

Protein-protein interaction data from IntAct, MINT, BioGRID, DIP, HPRD, MIPS/MPact

Protein annotations from UniProt, Ensembl, WormBase BioMart