%0 Journal Article %J Genome Biol %D 2013 %T Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. %A Megraw, Molly %A Mukherjee, Sayan %A Ohler, Uwe %K Algorithms %K Animals %K Arabidopsis %K Computational Biology %K Drosophila melanogaster %K Gene Expression Regulation %K Gene Regulatory Networks %K Humans %K MicroRNAs %K Molecular Sequence Annotation %K Nucleic Acid Conformation %K Software %K Transcription Factors %X

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.

%B Genome Biol %V 14 %P R85 %8 2013 %G eng %N 8 %R 10.1186/gb-2013-14-8-r85