CoRegNet: reconstruction and integrated analysis of co-regulatory networks.

ABSTRACT

UNLABELLED CoRegNet is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, CoRegNet can be used to reconstruct a large-scale co-regulatory network, integrate regulation evidences such as transcription factor binding sites and ChIP data, estimate sample-specific regulator activity, identify cooperative transcription factors and analyze the sample-specific combinations of active regulators through an interactive visualization tool. In this study CoRegNet was used to identify driver regulators of bladder cancer. AVAILABILITY: CoRegNet is available at http//bioconductor.org/packages/CoRegNet CONTACT remy.nicolle@issb.genopole.fr or mohamed.elati@issb.genopole.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.