Work

Analyzing Protein–Protein Interaction Networks

Year: 2012

Type: review

Abstract: The advent of the "omics" era in biology research has brought new challenges and requires the development of novel strategies to answer previously intractable questions. Molecular interaction networks provide a framework to visualize cellular processes, but their complexity often makes their interpretation an overwhelming task. The inherently artificial nature of interaction detection methods and the incompleteness of currently available interaction maps call for a careful and well-informed utilization of this valuable data. In this tutorial, we aim to give an overview of the key aspects that any researcher needs to consider when working with molecular interaction data sets and we outline an example for interactome analysis. Using the molecular interaction database IntAct, the software platform Cytoscape, and its plugins BiNGO and clusterMaker, and taking as a starting point a list of proteins identified in a mass spectrometry-based proteomics experiment, we show how to build, visualize, and analyze a protein-protein interaction network.

Source: Journal of Proteome Research

DOI: 10.1021/pr201211w

Authors: Gavin C. K. W. Koh, Pablo Porras, Bruno Aranda, Henning Hermjakob, Sandra E. Orchard

Institutions: European Bioinformatics Institute, University of Cambridge, Wellcome Trust

Language: English

Topic: Bioinformatics and Genomic Networks

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funder: Wellcome Trust

Award: The effect of diabetes mellitus and glibenclamide on the immunopathogenesis of melioidosis.