Exploring Expression Ratios

1. Use the command Merge Expression Files to combine the existing expression file derisi_first5.exp and the existing expression file derisi_last2.exp. Be sure to list the files in this order, and change the nicknames for both files to t. Call the merged file derisi.exp. After the merge is complete, examine derisi.exp using View / Edit Data, to be sure the column labels are in order.
2. Add the gene information in yeastgenes.info to derisi.exp, forming derisi_i.exp. Use this merged and annotated file, which is the complete time course published by DeRisi, to answer the remaining questions.
3. How many genes' expression change by at least a factor of 2 in the first two hours? (p. 680) Answer
4. How many genes' expression are greater than 2.0 or less than 0.5 in the time 0 microarray? How does this affect your interpretation of the answer to #3? Answer
5. How many genes' expression increases by a factor of at least 4 sometime during the time course? How many genes' expression diminishes by a factor of at least 4 sometime during the time course? (p. 680) Answer
6. Investigate the change in expression of ribosomal genes by forming a group of ribosomal genes, plotting the group, and highlighting the mitochrondrial genes in the plot. (p. 681) Answer
7. Find genes with the "late induction profile" described on p. 681, and graphed in Fig. 5B, in which levels increased by more than ninefold at the last timepoint, but less than threefold at the preceding timepoint. Compare your results to those in Fig. 5B, and use http://www.yeastgenome.org to help explain any discrepencies. Answer
8. Add the file derisi_lab_ i_tlog2.dis to the project to enable you to answer the remaining questions. This file was generated by transforming the ratios with log base 2 , then computing dissimilarities using 1-correlation. The process of computing dissimilarities takes a few hours, even on a fast computer, so we are skipping this step for this lab. If you do not have the file, you can download it by right-clicking here. WARNING, this file is HUGE (72 MB)!
9. Form a supervised cluster with SAM1 (YLR180W) as the seed, and compare your results to Fig 5E,
   1. using 0.2 as the threshold. Answer
   2. using 0.02 as the threshold. Answer
10. If you did not know what patterns to expect or search for, you might want to cluster the genes in to groups with similar patterns first. Use the (unsupervised) QT clust method with a threshold of 0.3 and maximum number of clusters 20. Answer

This concludes the online lab, "Exploring Diauxic Shift Microarray Data with MAGIC Tool."

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