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Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007

Rhythmic growth explained by coincidence between internal and external cues; what gene networks are underlying?. Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007. Acknowledgements. Stacey Hamer. Maloof lab. Julin Maloof.

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Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007

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  1. Rhythmic growth explained by coincidence between internal and external cues;what gene networks are underlying? Kazunari (Kazu) Nozue College of Biological Sciences, University of California Davis May 16, 2007

  2. Acknowledgements Stacey Hamer Maloof lab Julin Maloof Andreah Wallace (Andii) Mike Covington

  3. protein-gene interactions PROTEOME protein-protein interactions METABOLISM Bio-chemical reactions Citrate Cycle Cellular networks: GENOME

  4. complex network regulates growth light GA Growth clock Brassino -steroid ethylene auxin Nozue & Maloof (2006)

  5. Molecular mechanisms of circadian clock negative feedback loop Salome (2005)

  6. Hypocotyl elongation has circadian rhythm Time in continuous light (hrs) 2d 12L/12D entrainment image recording under continuous dim light Dowson-Day (1999) Plant J. 17:63-71

  7. circadian clock controls hypocotyl elongation rhythm clock-deficient mutant wild type Time in continuous light (hrs) Dowson-Day (1999) Plant J. 17:63-71

  8. Real world is not continuous light…day-night cycles!

  9. time-lapse photography (Col; short day (SD))

  10. what molecular mechanisms are underlying? Hypothesis: transcriptional regulation is involved in gating of dark-induced elongation. Method: whole genome microarray analysis Purpose: to find genes which expression patterns are correlated with growth pattern

  11. what is microarray?

  12. TOP 10 of up-regulated genesin growing phase (Dark) vs non-growing phase (Dark) rank-product non-parmetric method(Breitling 2004, FEBS 573:83) pfp; percentage of false-positives, FC; fold-change Nozue (2007) Nature

  13. Rhythmic growth explained by coincidence between internal and external cues WT Nozue (2007) Nature

  14. coincidence between internal & external cuesanother example: flowering time Imaizumi (2006)

  15. questions what are genes in my lists? Do the genes control growth? If so, how they control growth?

  16. what gene networks control plant growth? genotype interaction (cf. Jose’s talk) protein-protein interaction co-expression

  17. PIF4 visualization of network PIL6 non-overlapping of each gene network UPG; green UPNG; magenta

  18. visualization of network what are other genes? <plan> GO annotation Gene Ontology (GO) terms (Camon et al., 2004) what GO terms over-represented in these genes? GOHyperG function in R MapMan analysis? UPG; green UPNG; magenta

  19. partitioning of network how many groups are there? spectral method eigen vector/matrix betweeness (needs to learn more) UPG; green UPNG; magenta

  20. partitioning of network how many groups are there? spectral gap method  minus in eigen vector 2: blue circle plus in eigen vector 2; red circle Most of each component is overlapped with UPG or UPNG network. UPG; green UPNG; magenta

  21. protein-gene interactions PROTEOME protein-protein interactions METABOLISM Bio-chemical reactions Citrate Cycle Cellular networks: GENOME

  22. biological network layered

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