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

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...

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Main Authors:	Megraw, Molly, Mukherjee, Sayan, Ohler, Uwe
Format:	Online
Language:	English
Published:	BioMed Central 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054853/

id	pubmed-4054853
recordtype	oai_dc
spelling	pubmed-40548532014-06-12 Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits Megraw, Molly Mukherjee, Sayan Ohler, Uwe Method 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. BioMed Central 2013 2013-08-23 /pmc/articles/PMC4054853/ /pubmed/23972209 http://dx.doi.org/10.1186/gb-2013-14-8-r85 Text en Copyright © 2013 Megraw et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Megraw, Molly Mukherjee, Sayan Ohler, Uwe
spellingShingle	Megraw, Molly Mukherjee, Sayan Ohler, Uwe Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
author_facet	Megraw, Molly Mukherjee, Sayan Ohler, Uwe
author_sort	Megraw, Molly
title	Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
title_short	Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
title_full	Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
title_fullStr	Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
title_full_unstemmed	Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
title_sort	sustained-input switches for transcription factors and micrornas are central building blocks of eukaryotic gene circuits
description	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.
publisher	BioMed Central
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054853/
_version_	1612100132663197696

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

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