TY - JOUR T1 - Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. JF - Genome Biol Y1 - 2013 A1 - Megraw, Molly A1 - Mukherjee, Sayan A1 - Ohler, Uwe KW - Algorithms KW - Animals KW - Arabidopsis KW - Computational Biology KW - Drosophila melanogaster KW - Gene Expression Regulation KW - Gene Regulatory Networks KW - Humans KW - MicroRNAs KW - Molecular Sequence Annotation KW - Nucleic Acid Conformation KW - Software KW - Transcription Factors AB -

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.

VL - 14 IS - 8 ER -