Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
| dc.contributor.author | Megraw, Molly | |
| dc.contributor.author | Mukherjee, Sayan | |
| dc.contributor.author | Ohler, Uwe | |
| dc.coverage.spatial | England | |
| dc.date.accessioned | 2015-09-03T06:40:34Z | |
| dc.date.issued | 2013-08-23 | |
| dc.description.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. | |
| dc.identifier | ||
| dc.identifier | gb-2013-14-8-r85 | |
| dc.identifier.eissn | 1474-760X | |
| dc.identifier.uri | ||
| dc.language | eng | |
| dc.publisher | Springer Science and Business Media LLC | |
| dc.relation.ispartof | Genome Biol | |
| dc.relation.isversionof | 10.1186/gb-2013-14-8-r85 | |
| dc.subject | Algorithms | |
| dc.subject | Animals | |
| dc.subject | Arabidopsis | |
| dc.subject | Computational Biology | |
| dc.subject | Drosophila melanogaster | |
| dc.subject | Gene Expression Regulation | |
| dc.subject | Gene Regulatory Networks | |
| dc.subject | Humans | |
| dc.subject | MicroRNAs | |
| dc.subject | Molecular Sequence Annotation | |
| dc.subject | Nucleic Acid Conformation | |
| dc.subject | Software | |
| dc.subject | Transcription Factors | |
| dc.title | Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. | |
| dc.type | Journal article | |
| pubs.author-url | ||
| pubs.begin-page | R85 | |
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| pubs.issue | 8 | |
| pubs.organisational-group | Basic Science Departments | |
| pubs.organisational-group | Biostatistics & Bioinformatics | |
| pubs.organisational-group | Duke | |
| pubs.organisational-group | School of Medicine | |
| pubs.publication-status | Published online | |
| pubs.volume | 14 |
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