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

Genome Biol. 2013 Aug 23;14(8):R85. doi: 10.1186/gb-2013-14-8-r85.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Animals
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Computational Biology
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Molecular Sequence Annotation
  • Nucleic Acid Conformation
  • Software*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • MicroRNAs
  • Transcription Factors