LauraTerada Individual Journal Assignment Week 12

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Clustering and Gene Ontology Analysis with STEM

Downloading and extracting the STEM software

Prepare your microarray data to fit 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 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

  1. What are the top 10 transcription factors in your results? List them on your wiki page with the percent of the genes in your cluster that they each regulate.
    • Ste12p 42.4 %; Sok2p 27.2%; Rap1p 25.6%; Skn7p 19.2%; Fhl1p 16.8%; Mbp1p 16.0%; Yap5p 15.2%; Cin5p 15.2%; Tec1p 14.4%; Pdr1p 14.4%
  2. Are Cin5, Gln3, Hmo1, and Zap1 on the list? What percentage of the genes in the cluster does they each regulate? How many genes does they each regulate?
    • Cin5: 15.5%, 19 genes; Gln3 2.4%, 3 genes; Zap1 1.6%, 2 genes
  3. Which transcription factors do you want to add to the model and why?
    • Ste12p, Sok2p, Rap1p, Yap5p, Tec1p because these transcription factors are on the list in the top 10.

Regulation Matrix Excel dCIN5 Screenshots