Module 1: Is the hourglass model for gene expression really supported by the data?

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  • Title: "Is the hourglass model for gene expression really supported by the data?"
  • Paper to be examined: “A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns”, Nature 9;468(7325):815-8 (2010)[1]
  • Key claim of the paper: "Gene expression follows the so-called hour-glass pattern observed for morphological features of development, which are most similar to each other in the phylotypic stage in mid-development."
  • Schedule:
    • H1: General introduction to the paper/motivation
    • H2-3: Write code to import the data and start computing transcriptome age index (TAI)
    • H4-6: Aim to reproduce figure 1 of the paper – help/scripts will be given if needed.
    • H7: Discussion: “Are you convinced of this result? What might have gone wrong?”
    • H8: Redo analysis using log-transformed data
    • H9: Summarize results (e.g. on this wiki)
  • Key bioinformatics concept of this module: "Data normalization is important and can impact the results of subsequent analyses!"