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Bioinformatics. 2015 Sep 15;31(18):3066-8. doi: 10.1093/bioinformatics/btv305. Epub 2015 May 14.

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

Author information

1
iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.
2
iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.
3
iSSB, CNRS, University of Evry, Genopole, 91030 Evry Cedex, France, Institut Curie, PSL Research University, 75248 Cedex 05, France and CNRS UMR144, 75248 Cedex 05, France.

Abstract

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.

PMID:
25979476
PMCID:
PMC4565029
DOI:
10.1093/bioinformatics/btv305
[Indexed for MEDLINE]
Free PMC Article

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