Case Study: NASCarray 157 Effect of CO2 and Light

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Case Study NASCarray 157Effect of CO2 and
(Light)
MRes in AGPS

• Hung-Ming Lai
• stxhml_at_nottingham.ac.uk
• ID 4087152
• 31 October 2008

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Outline

• Prior Knowledge
• Data Preparation
• Visually Comparing Expression Data
• Data Analysis
• Hunting Information/Uncovering

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Prior Knowledge

• Stomata
• Environmental Signals
• Plant Development
• Correlations between Stomata and External Signals
• Stomatal density ? Light intensity
• CO2 concentration ? ?2 ? Stomatal density ? 30
• Lake, J.A., Quick, W.P., Beerling, D.J. and
  Woodward, F.I. (2001). Signals from mature to new
  leaves. Nature, 411, 154.
• http//www.nature.com/nature/journal/v411/n6834/fu
  ll/411154a0.htmlf1
• Looking at genetic level
• Systemic signalling of environmental cues in
  Arabidopsis leaves
• S. A. Coupe, B. G. Palmer, J. A. Lake,
  S. A. Overy, K. Oxborough, F. I. Woodward, J. E.
  Gray and W. P. Quick. (2006). Journal of
  Experimental Botany, Vol. 57, No. 2, pp. 329341

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What does the data set look like
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Description and Interpretation of the data
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Visually Comparing Expression Data 1
2-fold change for all comparison
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Visually Comparing Expression Data 2
2, 24
12, 24
VS
Time independent ?
What about this ?
24, 96
48, 96
VS
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Data analysis 1

• Factor in gene regulation
• CO2 ambient, high
• Light ambient, low (shade)
• Time Point 2,4,12,24,48,96
• Approach
• Complicated or Naïve
• Efficient and Effective
• The other thinking Clustering
• How?

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Data analysis 2

• Pick up informative profiles regarding CO2
• Filtering out genes which doesnt change their
  expression level in any time/CO2 condition
• Get relevant genes by Venn Diagram
• Dual-clustering
• Clustering on genes Gene tree
• Effect of CO2 on molecular level
• Potential regulatory sequence
• Time dependent or independent
• Clustering on sample Condition tree
• Which factor is more significant?

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Filter on expression level
Genes
22,810

• Put all genes into expression profiles
• Get rid of irrelevant data
• Venn Diagram
• Collect those informative genes

22,602
208
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Gene Tree
CO2 Experiment (14 conds)
Default Experiment (28 conds)
Time Dependent
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Gene Expression Change
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More Finding

• K-mean Algorithm

• Regulatory Sequence
• (CO2 Exp)

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Condition Tree

• Again, uncovering the informative genes relative
  to CO2 and Light , i.e. CO2 ? Light, based on
  expression level
• Significance Light gt Time gt CO2
• Interaction?

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Uncovering Gene Ontology
Up-regulated DL
Informative DL
Informative ML
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Uncovering more likely 2-factor Genes
2-way ANOVA Analysis
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Uncovering - Pathway

• Gene 254283_s_at
• One of 2-factor genes
• Pathway Flavonoid biosynthesis

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Uncovering find similar gene(254283-s-at)
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Conclusion

• A Feasible Approach
• Not fragmental but Integrative instead
• Exploring the effect of CO2 concentration on gene
  expression level
• Finding some slight correlations between CO2,
  time points, and light intensity
• Uncovering on ontology, pathway and the similar
  gene

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Future Work

• Further analyses/work on the interaction
• Does any key gene/promoter/enhancer dominating
  the interaction
• Model the effect of those external signals on the
  system level