A system for generating transcription regulatory networks with combinatorial control of transcription

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Abstract
Summary: We have developed a new software system, REgulatory Network generator with COmbinatorial control (RENCO), for automatic generation of differential equations describing pre-transcriptional combinatorics in artificial regulatory networks. RENCO has the following benefits: (a) it explicitly models protein–protein interactions among transcription factors, (b) it captures combinatorial control of transcription factors on target genes and (c) it produces output in Systems Biology Markup Language (SBML) format, which allows these equations to be directly imported into existing simulators. Explicit modeling of the protein interactions allows RENCO to incorporate greater mechanistic detail of the transcription machinery compared to existing models and can provide a better assessment of algorithms for regulatory network inference. Availability: RENCO is a C++ command line program, available at http://sourceforge.net/projects/renco/ Contact: terran@cs.unm.edu Supplementary information: Supplementary data are available at Bioinformatics online.