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Effects of Clioquinol on yeast

Analyze the microarray dataset made available by the following study: https://www.ncbi.nlm.nih.gov/pubmed/21504115 clioquinol.yeast.Li2010.pdf

The microarray data is available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17257

  • Apply a normalization method of your choice, so the expression values of samples become comparable.
  • Write a function that replaces GSE probe ids with the gene symbols present in the GPL.
  • Show a hierarchical clustering of samples. (Just a hierarchical clustering (ie a dendrogram) of samples, not a heatmap of expression values.)
  • Show a clustergram (heatmap, combined with clustering of samples and clustering of genes) of expression values.
  • Report the top 10 most different genes between the Clioquinol and control groups.
  • Report the functional annotations (GO Biological Processes and KEGG Pathways) that are significantly different between the two groups.
  • Discuss whether your results align with the findings reported in the paper.
  • 5% of your grade is for optimizing download & parse functions. If you do optimize, describe your optimizations as comments in your main notebook.