Sustained-input switches for transcription factors and microRNAs are central
building blocks of eukaryotic gene circuits
#MMPMID23972209
Megraw M
; Mukherjee S
; Ohler U
Genome Biol
2013[Aug]; 14
(8
): R85
PMID23972209
show ga
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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