Inferring modules from human protein interactome classes.

BMC Systems Biology
Elisabetta MarrasEnrico Capobianco

Abstract

The integration of protein-protein interaction networks derived from high-throughput screening approaches and complementary sources is a key topic in systems biology. Although integration of protein interaction data is conventionally performed, the effects of this procedure on the result of network analyses has not been examined yet. In particular, in order to optimize the fusion of heterogeneous interaction datasets, it is crucial to consider not only their degree of coverage and accuracy, but also their mutual dependencies and additional salient features. We examined this issue based on the analysis of modules detected by network clustering methods applied to both integrated and individual (disaggregated) data sources, which we call interactome classes. Due to class diversity, we deal with variable dependencies of data features arising from structural specificities and biases, but also from possible overlaps. Since highly connected regions of the human interactome may point to potential protein complexes, we have focused on the concept of modularity, and elucidated the detection power of module extraction algorithms by independent validations based on GO, MIPS and KEGG. From the combination of protein interactions with gene e...Continue Reading

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Citations

Oct 17, 2015·Scientific Reports·Bing LiYongyan Wang
Nov 20, 2014·Computational and Structural Biotechnology Journal·Enrico Capobianco
Jul 8, 2016·Molecular & Cellular Proteomics : MCP·Paul AshfordMaya Topf

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Methods Mentioned

BETA
two hybrid

Software Mentioned

Matlab
BIOGRID
MCODE2coresINT
Ortho
UniHi
MCODE2coresHTP
R
INTACT
igraph
MaxMod

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