LauraTerada Individual Journal Assignment Week 12

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Revision as of 12:51, 9 April 2013

Contents

Clustering and Gene Ontology Analysis with STEM

Downloading and extracting the STEM software

Prepare your microarray data to fit STEM

Run STEM

View and Save STEM Results

Analyzing and Interpreting STEM Results

  1. Select one of the profiles you saved in the previous step for further intepretation of the data.
    • Why did you select this profile? In other words, why was it interesting to you?
      • I chose profile 2 because it shows distinct down regulation up to 60 min (first three time points), and after that there is clear up regulation.
    • How many genes belong to this profile?
      • 126.0 genes
    • How many genes were expected to belong to this profile?
      • 49.8 genes
    • What is the p value for the enrichment of genes in this profile?
      • 2.9E-20 (significant)
    • How many GO terms are associated with this profile at p < 0.05?
      • 4
    • How many GO terms are associated with this profile with a corrected p value < 0.05?
      • 0
    • Select 10 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05). Look up the definitions for each of the terms at http://geneontology.org. Write a paragraph that describes the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms?
      • GO:0005886 (plasma membrane)
      • GO:0071944 (cell periphery)
      • GO:0031225 (anchored to membrane)
      • GO:0031224 (intrinsic to membrane)

Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes

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