Analyzing Protein-Protein Interaction Networks with Web Tools

Charalampos      N. Moschopoulos; Georgios      A. Pavlopoulos; Spiridon      Likothanassis; Sophia      Kossida

Abstract

Protein-protein interactions (PPIs) have been marked as the main actors for all of the processes taking place in a cell and therefore great efforts have been made towards the understanding of their biological function. Today, new highthroughput technologies generate vast amounts of interaction data even with a limited number of experiments. The analysis of these data can lead to valuable conclusions about the cell organization such as protein complex detection, characterization of protein function, identification of protein pathways etc. Various techniques have been applied to analyze PPI data based on different strategies. Web interfaces that have been developed to host these methods consist of valuable tools which are often available to all users. In this review, we describe a collection of such web tools to analyze PPI data and more that are applicable to a wider range of problems. The functionality of each web tool is described as well as their compatibility with other resources. An overview of the technologies that are supported by such tools for their activities is also provided.

Keywords: Protein graph analysis, protein network, protein-protein interactions (PPIs), web tools, NeAT, VisANT, STRING, Network BLAST, SNOW, ProCope, PINA, Hubba, tYNA