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

*  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)[http://www.nature.com/nature/journal/v468/n7325/full/nature09632.html] 

* 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." 

* Data and Code: [[Media:danio_age_index.txt.zip]] [[Media:ProcessedMicroarrayData.txt.zip]]
  
* Schedule: 
** H1: General introduction to the paper/motivation (slides: [[Media:IntroductionM1.pptx]])
** 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: Wrap-up

* Key bioinformatics concept of this module: "Data normalization is important and can impact the results of subsequent analyses!"

* back to [[UNIL MSc course: "Case studies in bioinformatics"]]