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

dc.contributor.author Megraw, M
dc.contributor.author Mukherjee, Sayan
dc.contributor.author Ohler, Uwe
dc.coverage.spatial England
dc.date.accessioned 2015-09-03T06:40:34Z
dc.date.issued 2013-08-23
dc.identifier http://www.ncbi.nlm.nih.gov/pubmed/23972209
dc.identifier gb-2013-14-8-r85
dc.identifier.uri http://hdl.handle.net/10161/10584
dc.description.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.
dc.language eng
dc.relation.ispartof Genome Biol
dc.relation.isversionof 10.1186/gb-2013-14-8-r85
dc.subject Algorithms
dc.subject Animals
dc.subject Arabidopsis
dc.subject Computational Biology
dc.subject Drosophila melanogaster
dc.subject Gene Expression Regulation
dc.subject Gene Regulatory Networks
dc.subject Humans
dc.subject MicroRNAs
dc.subject Molecular Sequence Annotation
dc.subject Nucleic Acid Conformation
dc.subject Software
dc.subject Transcription Factors
dc.title Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
dc.type Journal article
pubs.author-url http://www.ncbi.nlm.nih.gov/pubmed/23972209
pubs.begin-page R85
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pubs.issue 8
pubs.organisational-group Basic Science Departments
pubs.organisational-group Biostatistics & Bioinformatics
pubs.organisational-group Duke
pubs.organisational-group School of Medicine
pubs.publication-status Published online
pubs.volume 14
dc.identifier.eissn 1474-760X


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