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

http://ir.library.oregonstate.edu/concern/articles/z316q5941

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central Ltd. The published article can be found at:  http://genomebiology.com/. Supporting Information can be found at:  http://genomebiology.com/2013/14/8/R85/additional

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  • 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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  • Megraw, M., Mukherjee, S., & Ohler, U. (2013). Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biology, 14(8), R85. doi:10.1186/gb-2013-14-8-r85
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  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-03-05T23:14:44Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) MegrawMollyBotanyPlantPathologySustained-InputSwitches.pdf: 1072148 bytes, checksum: fc3bbc5ef1f1828e1366455e5edfcaee (MD5)
  • description.provenance : Made available in DSpace on 2014-03-05T23:14:44Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) MegrawMollyBotanyPlantPathologySustained-InputSwitches.pdf: 1072148 bytes, checksum: fc3bbc5ef1f1828e1366455e5edfcaee (MD5) Previous issue date: 2013
  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-03-04T22:50:59Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) MegrawMollyBotanyPlantPathologySustained-InputSwitches.pdf: 1072148 bytes, checksum: fc3bbc5ef1f1828e1366455e5edfcaee (MD5)

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