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

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https://ir.library.oregonstate.edu/concern/articles/z316q5941

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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.
  • Keywords: gene regulation, transcription factor, microRNA, network motif
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  • Megraw, M., Mukherjee, S., & Ohler, U. (2013). Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biology, 14(8), R85. doi:10.1186/gb-2013-14-8-r85
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  • 14
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  • 8
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  • UO is funded by awardsfrom the NSF (MCB-0822033) and NIH (P50 GM 081883). MM was supportedby an NSF Postdoctoral Fellowship in Biological Informatics (#0805648) andan NIH K99-R00 Pathway to Independence Award GM097188.
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