Data Analysis Using Genespring

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Data Analysis Using Genespring

• Keren Turner

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Introduction

• Experiment Circadian expression of genes
  modelling the Arabidopsis circadian clock
• Preparation
• 7 days at 22C
• Cycles of 12 hours white light, 12 hours
  darkness.
• Transferred to constant white light at 22 C

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Dataset

• Tissue harvested every 4 hours over two days
• Internal Replicates
• Total of 13 samples
• 26 hours
• 30, 34, 38, 42, 46, 50
• 54, 58, 62, 66, 70, 74

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What information?

• Which genes are expressed during the different
  circadian clock phases?
• Is the difference of the gene expression within
  these phases significant?
• What do these genes regulate?

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Analysis

• Genespring
• 22, 810 genes in experiment
• Quality Control
• Filter on expression
• Minimum intensity value 50
• Values appear in 6 of 13 conditions
• 17, 592 genes pass filter

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Filter on Expression Level

• Physical Position
• All Genes
• Before Filter

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Filter on Expression Level

• Physical Position
• Quality Control Genes
• After Filter

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Analysis

• Differential expression of genes in time points
• Filter on Fold Change
• Genes upregulated 2-fold in 12 time points,
  compared to control time
• 31 genes of the 17, 592 pass the filter

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Filter on Fold Change
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Filter on Fold Change
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Analysis

• Statistical significance
• ANOVA
• 17, 592 genes in QC data
• 631 changes statistically significant
• 31 genes in 2-fold upregulated from time 0
• 31 changes statistically significant

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Analysis results

• Filter on Fold Change
• Difference in expression of genes within the
  different time points compared to the genes
  expressed at 26 hours
• 31 genes regulated by the circadian clock?

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K means clustering

• Genes are placed in clusters according to
  expression patterns
• Shows upregulation and downregulation of genes in
  time dependent manner

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K means clustering
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Spreadsheet
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Analysis results

• What do these genes regulate?

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Linking genes to circadian clock

• Condition Tree

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Conclusion

• 22,810 genes originally reported for this
  experiment
• 31 genes upregulated from time 0 (26 hours)
• 17 different types of genes
• Expressed at differing levels throughout the
  circadian clock