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

Journal Article (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.

Full Text

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

  • PMC4054853

Electronic International Standard Serial Number (EISSN)

  • 1474-760X

Digital Object Identifier (DOI)

  • 10.1186/gb-2013-14-8-r85


  • eng

Conference Location

  • England