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BioMed Central, Genome Biology, 8(14), p. R85

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

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

Journal article published in 2013 by Molly Megraw ORCID, Sayan Mukherjee, Uwe Ohler
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract 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.