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

TitleSustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Publication TypeJournal Article
Year of Publication2013
AuthorsMegraw, M, Mukherjee, S, Ohler, U
JournalGenome Biol
Volume14
Issue8
PaginationR85
Date Published2013
ISSN1474-760X
KeywordsAlgorithms, Animals, Arabidopsis, Computational Biology, Drosophila melanogaster, Gene Expression Regulation, Gene Regulatory Networks, Humans, MicroRNAs, Molecular Sequence Annotation, Nucleic Acid Conformation, Software, Transcription Factors
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.

DOI10.1186/gb-2013-14-8-r85
Alternate JournalGenome Biol.
PubMed ID23972209
PubMed Central IDPMC4054853
Grant ListGM097188 / GM / NIGMS NIH HHS / United States
P50 GM 081883 / GM / NIGMS NIH HHS / United States
R00 GM097188 / GM / NIGMS NIH HHS / United States