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• W1965107569 endingPage "e3105" @default.
• W1965107569 startingPage "e3105" @default.
• W1965107569 abstract "A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2) that encode a transcriptional activator (as well as a blue-light receptor) and an oscillator frequency (frq) that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE), based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid) biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2) control were resolved into four classes, circadian only (612 genes), light-responsive only (396), both circadian and light-responsive (328), and neither circadian nor light-responsive (987). In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes." @default.
• W1965107569 created "2016-06-24" @default.
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• W1965107569 date "2008-08-29" @default.
• W1965107569 modified "2023-10-07" @default.
• W1965107569 title "Systems Biology of the Clock in Neurospora crassa" @default.
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• W1965107569 doi "https://doi.org/10.1371/journal.pone.0003105" @default.
• W1965107569 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2518617" @default.
• W1965107569 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18769678" @default.
• W1965107569 hasPublicationYear "2008" @default.

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