Network biology

ENIGMA

Enigma is a software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. The tool has a built-in visualization tool to allow for a straightforward interpretation of the different regulatory modules.

LeMoNe

LeMoNe is a software package for inferring regulatory modules networks and their specific regulators from gene expression data using a two-way Bayesian clustering of genes and conditions. LeMoNe can handle heterogeneous regulators such as discrete data and/or microRNA expression data, and also allows for annotating modules with GO categories. The tool also has a built-in visualization tool for an easy interpretation of the inferred modules.

Network Motif Clustering Toolbox

The Network Notif Clustering Toolbox is a Matlab/Octave toolbox for clustering topological network motifs in large-scale, integrated networks. The clustering algorithm is based on rigorous mathematical results and has been validated on an integrated yeast interaction network. See Michoel et al. for more information.

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