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


BACKGROUND
RENCO is a C++ command line program, available at http://sourceforge.net/projects/renco/
Roy
Sushmita
S
Department of Computer Science and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
Werner-Washburne
Margaret
M
Lane
Terran
T
D020650:Combinatorial Chemistry Techniques / Q000379:methods; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism*; D015533:Transcriptional Activation / Q000502:physiology*
D014157:Transcription Factors