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Lab8 - CSci 3003 Introduction to Computing in Biology Lab...

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CSci 3003: Introduction to Computing in Biology Lab Assignment #8 20 points Assigned: 4/7/10 Due: Tuesday, 4/27/10 (before midnight) Goals of this lab: Practice using Matlab to load/analyze expression data. Practice using software tools to explore and interpret a gene expression dataset. Lab 8: Exploring gene expression signatures through cluster analysis We will continue focusing on gene expression data, but address a different question than last week. Instead of looking for genes whose expression is different across two sets of samples (e.g. metastasis/non-metastasis), we will look for genes that have similar profiles of expression across large sets of samples. This can be a very powerful technique for discovering the function of uncharacterized genes. For example, two genes that are co-expressed together in response to several different environmental conditions are very likely to perform similar functions in the cell. The data from this lab are taken from the following study, which you can read about by clicking http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmed id=11102521 Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000 Dec;11(12):4241-57. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO.
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Part I: Understanding the gene expression study Just like last time, the first part of this lab will focus on understanding the gene expression study that was done. By following the link above (or simply using Google to find the study), open the paper associated with the data and read the paper’s abstract. Briefly answer the following questions ab out the study: (1) What was the purpose of the study and what experiments did the authors do to answer the question they were interested in? (2) What are some examples of different environments or stresses the authors subjected yeast cells to before measuring their gene expression? (3) Describe one of the significant conclusions of the study. Part II: Exploring the gene expression data with public software tools For this part of the lab, we will be using a software tool called Java Treeview, which is a software tool for visualizing gene expression clusters. You can download the tool at: http://sourceforge.net/project/showfiles.php?group_id=84593&package_id=87352&release_id=611720
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