Maere Lab | Evolutionary Systems Biology
BiNGO is a Java-based tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. BiNGO is implemented as a plugin for Cytoscape, which is a an open source bioinformatics software platform for visualizing and integrating molecular interaction networks.
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 the genes in the module.
LeMoNe is a software package for Learning Module Networks from gene expression data. Version 1.0 uses a heuristic technique to assign regulators to modules while version 2.0 uses a Gibbs sampling strategy to cluster genes and experiments, and a stochastic method to assign regulators to modules. Developed in collaboration with the Van de Peer lab.
PiNGO is a Java-based tool to find lead genes in biological networks, i.e. genes significantly associated with user-defined target processes. PiNGO is implemented as a plugin for Cytoscape, which is a an open source bioinformatics software platform for visualizing and integrating molecular interaction networks.