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 Julin Maloof Stacey Hamer Mike CovingtonAndreah Wallace (Andii) Maloof lab

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

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

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

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

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

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

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

11. 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

12. what is microarray?

13. TOP 10 of up-regulated genes in 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

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

15. coincidence between internal & external cues another example: flowering time Imaizumi (2006)

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

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

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

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

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

21. partitioning of network 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. how many groups are there? a.spectral gap method  UPG; green UPNG; magenta

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

23. biological network layered