PIANA: protein interactions and network analysis
Bioinformatics
Modular organization of protein interaction networks
Bioinformatics
Bioinformatics
Tools for visually exploring biological networks
Bioinformatics
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Here the authors review the state of the art in the use of protein-protein interactions ppis within the context of the interpretation of genomic experiments. They report the available resources and methodologies used to create a curated compilation of ppis introducing a novel approach to filter interactions. Special attention is paid in the complexity of the topology of the networks formed by proteins nodes and pairwise interactions edges. These networks can be studied using graph theory and a brief introduction to the characterization of biological networks and definitions of the more used network parameters is also given. Also a report on the available resources to perform different modes of functional profiling using ppi data is provided along with a discussion on the approaches that have typically been applied into this context. They also introduce a novel methodology for the evaluation of networks and some examples of its application.