GESTODifferent

GESTODifferent - A Cytoscape plugin for the identification of Gene Regulatory Networks describing the stochastic differentiation process

This Cytoscape plugin generates Noisy Random Boolean models of Gene Regulatory Networks, which are non-linear binary models introduced by Kauffman.

This plugin implements also a tree-matching algorithm to select those networks whose activation patterns can be related to a custom lineage differentiation tree, according to the approach defined in Villani et al., PLoS ONE 6(3):e17703 (2011).

GESTODifferent produces reports and some standard network statistics such as clustering or bias coefficients, average connectivity and path length. This type of approach can be used to describe hierarchical, stochastic or deterministic differentiation processes as well as induced pluripotency.

At BIMIB, we used this tool to search for networks and parametrize a multiscale model of intestinal colon crypts

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling. A.Graudenzi, G.Caravagna, G.De Matteis, M.Antoniotti. PLoS ONE, 9(5):e97272, 2014.

Download

GESTODifferent has an official website.

This tool has now a follow up: CABERNET.

Reference

GeStoDifferent: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process. M.Antoniotti, G.Bader, G.Caravagna, S.Crippa, A.Graudenzi, G.Mauri. Bioinformatics 29(4), 513-514, 2013.