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ProblemSet2doc - Introduction to Systems Biology Problem...

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Introduction to Systems Biology Problem Set 2 Due: Before Spring Break Only two problems this time. For the first problem, all I want are the answers to the included questions. For the second problem, please put your answers to the questions on one page, the graph on a second page, and then include your well commented code beginning with a section that describes how your program works. The results must be turned in via the digital drop box. 1) The Yeast Cell Cycle As we discussed in class, one of the earliest (if not the earliest) applications of micro-arrays was the identification of the genes involved in the cell cycle in yeast. The original data for that experiment can be found at http://genome-www.stanford.edu/cellcycle/data/rawdata/ For this assignment, we’ll be taking a semi-guided tour through the original dataset in Matlab 1 . In this example/problem, the matlab commands will be in italics . The original micro-array images and the spreadsheets for data resulting from image analysis can be found at the above website. This original data-analysis step is extremely important, but its also very tiresome. So we’ll skip it. Go ahead and load the matlab formatted version of the data as found on Blackboard using the command load cellcycle.mat The file contains three items. The first, ccgene, contains a list of all of the yeast genes being analyzed. The remaining objects, ccvalues and time, contain, respecitively, the expression values of the genes and the time (in hours) that the RNA was sampled for analysis on the microarray. Let’s go ahead and examine the first gene: ccgene{1} plot(time, ccvalues(1,:)) xlabel (‘Time (Hours)’); ylabel(‘Log2 Relative Expression Level’); OK, that’s not very interesting, I admit. You can imagine examining each of the thousands of genes in the dataset in this manner, but then we wouldn’t be doing systems 1 For this assignment, you will need the Bioinformatics tool box, which can be found on most, if not all, of the campus clusters such as TEER.
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biology. What we are going to do for the remainder of this problem is demonstrate a method for analyzing the actions of all genes at once. Issue Number 1: Missing Data
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ProblemSet2doc - Introduction to Systems Biology Problem...

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