|Title||Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.|
|Publication Type||Journal Article|
|Year of Publication||2013|
|Authors||Megraw, M, Mukherjee, S, Ohler, U|
|Keywords||Algorithms, Animals, Arabidopsis, Computational Biology, Drosophila melanogaster, Gene Expression Regulation, Gene Regulatory Networks, Humans, MicroRNAs, Molecular Sequence Annotation, Nucleic Acid Conformation, Software, Transcription Factors|
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.
|Alternate Journal||Genome Biol.|
|PubMed Central ID||PMC4054853|
|Grant List||GM097188 / GM / NIGMS NIH HHS / United States |
P50 GM 081883 / GM / NIGMS NIH HHS / United States
R00 GM097188 / GM / NIGMS NIH HHS / United States
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Submitted by Megraw Lab Admin on Tue, 2016-07-12 22:10