CoRegNet: reconstruction and integrated analysis of co-regulatory networks.
basic_science · Level V
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- Record sourced from PubMed, PMID 25979476.
- Also identified by DOI 10.1093/bioinformatics/btv305 and PMC identifier 4565029.
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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. CoRegNet is available at http://bioconductor.org/packages/CoRegNet remy.nicolle@issb.genopole.fr or mohamed.elati@issb.genopole.fr Supplementary data are available at Bioinformatics online.
Medical subject headings
- Computational Biology
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- High-Throughput Nucleotide Sequencing
- Software
- Transcription Factors
- Urinary Bladder Neoplasms