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

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Official URL:https://doi.org/10.1186/gb-2013-14-8-r85
PubMed:View item in PubMed
Creators Name:Megraw, M. and Mukherjee, S. and Ohler, U.
Journal Title:Genome Biology
Journal Abbreviation:Genome Biol
Volume:14
Number:8
Page Range:R85
Date:23 August 2013
Keywords:Gene Regulation, microRNA, Network Motif, Transcription Factor, Animals, Drosophila Melanogaster
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.
ISSN:1465-6906
Publisher:BioMed Central (U.K.)
Item Type:Article

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