Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits

Genome Biology

Uwe Ohler²  Sayan Mukherjee¹  Molly Megraw³ 

[1] Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, USA;Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany;Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, OR, USA

关键词: transcription factor;    network motif;    microRNA;    gene regulation;   

Others  :  864100
DOI  :  10.1186/gb-2013-14-8-r85

 received in 2013-07-13, accepted in 2013-08-23,  发布年份 2013

【 摘 要 】

WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.

【 授权许可】

   
2013 Megraw et al.; licensee BioMed Central Ltd.

【 图 表 】

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