UNLABELLED SpotXplore is a plugin for Cytoscape for extraction and visualization of differentially expressed subnetworks (hotspots) from gene networks. The hotspot-based visualization approach enables interactive exploration of regulatory interactions in differentially expressed gene sets, and it allows a researcher to explore gene expression in direct relation to the affected cellular gene net...

There were errors published in Development 142, 3151-3165.In the issue published online on 22 September 2015, Fig. 3 was mislabelled: panels A, B, C and D should have been B, C, D and A, respectively. In the legend, the text prior to ‘(A) Cytoscape enrichment map…’ should not have been included. The correct version of the figure and legend now appear online and in print.We apologise to the auth...

Description This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disea...

ModuLand plug-in for Cytoscape: An algorithm for the determination of extensively overlapping modules, community centrality and its use in biological networks Máté Szalay-Bekő and Robin Palotai, Balázs Szappanos, István A. Kovács, Balázs Papp and Peter Csermely Department of Medical Chemistry, Semmelweis University, Budapest, Hungary Evolutionary Systems Biology Group, Biological Research Centr...