Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Published online
Journal Article
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.
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Duke Authors
Cited Authors
- Megraw, M; Mukherjee, S; Ohler, U
Published Date
- August 23, 2013
Published In
Volume / Issue
- 14 / 8
Start / End Page
- R85 -
PubMed ID
- 23972209
Pubmed Central ID
- 23972209
Electronic International Standard Serial Number (EISSN)
- 1474-760X
Digital Object Identifier (DOI)
- 10.1186/gb-2013-14-8-r85
Language
- eng
Conference Location
- England