Module 1: Is the hourglass model for gene expression really supported by the data?
From Computational Biology Group
- 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)
- 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."
- 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!"