title: Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
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.
authors: Molly
authors: M
authors: Megraw
authors: Sayan
authors: S
authors: Mukherjee
authors: Uwe
authors: U
authors: Ohler
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors
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