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

Bioinformatics
Sushmita RoyTerran Lane

Abstract

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. RENCO is a C++ command line program, available at http://sourceforge.net/projects/renco/

References

Dec 2, 2000·Physical Review Letters·R Albert, A L Barabasi
Oct 10, 2003·Bioinformatics·Pedro MendesKeying Ye
Nov 11, 2005·Physical Biology·Sergei Maslov, Kim Sneppen
Aug 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Archana BelleErin K O'Shea
Oct 13, 2006·Bioinformatics·Stefan HoopsUrsula Kummer
Nov 6, 2007·Bioinformatics·James Long, Mitchell Roth

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Citations

Oct 30, 2010·IET Systems Biology·S RoyT Lane
Feb 3, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Daniel MarbachDario Floreano
Mar 3, 2009·Bioinformatics·Hendrik HacheRalf Herwig
Sep 2, 2009·Microbiology and Molecular Biology Reviews : MMBR·Sacha A F T van HijumOscar P Kuipers
Oct 24, 2013·BMC Systems Biology·Janusz Sławek, Tomasz Arodź
Jun 26, 2021·Nature Communications·Robrecht CannoodtYvan Saeys

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Software Mentioned

ARACNE
RENCO
Copasi

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