Rhythmic growth explained by coincidence between internal and external cues what gene networks are u

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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

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Acknowledgements
Stacey Hamer
Maloof lab
Julin Maloof
Mike Covington
Andreah Wallace (Andii)
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Cellular networks
GENOME
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complex network regulates growth
light
GA
Growth
clock
Brassino -steroid
ethylene
auxin
Nozue Maloof (2006)
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(No Transcript)
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Molecular mechanisms of circadian clock
negative feedback loop
Salome (2005)
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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. 1763-71
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circadian clock controls hypocotyl elongation
rhythm
clock-deficient mutant
wild type
Time in continuous light (hrs)
Dowson-Day (1999) Plant J. 1763-71
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Real world is not continuous lightday-night
cycles!
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time-lapse photography (Col short day (SD))
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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

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what is microarray?
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TOP 10 of up-regulated genesin growing phase
(Dark) vs non-growing phase (Dark)

rank-product non-parmetric method(Breitling 2004,
FEBS 57383) pfp percentage of false-positives,
FC fold-change
Nozue (2007) Nature
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Rhythmic growth explained by coincidence between
internal and external cues
WT
Nozue (2007) Nature
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coincidence between internal external
cuesanother example flowering time
Imaizumi (2006)
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questions

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

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what gene networks control plant growth?

• genotype interaction (cf. Joses talk)
• protein-protein interaction
• co-expression

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visualization of network
PIF4
PIL6

• non-overlapping
• of each gene network

UPG green UPNG magenta
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visualization of network

• what are other genes?
• ltplangt
• 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
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partitioning of network

• how many groups are there?
• spectral method
• eigen vector/matrix
• betweeness (needs to learn more)

UPG green UPNG magenta
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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
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Cellular networks
GENOME
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biological network layered