Kasey E. O'Connor Week 12 Journal

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Clustering and Gene Ontology Analysis with STEM



  1. Why did you select this profile? In other words, why was it interesting to you?
    • I chose profile 45 because there was an large increase in gene expression within the first two time periods. I was curious to find out what genes are found on this profile, and what systems they are related to within the cell.
  2. How many genes belong to this profile?
    • 286
  3. How many genes were expected to belong to this profile?
    • 34.8
  4. What is the p value for the enrichment of genes in this profile?
    • 6.2x10-165
  5. How many GO terms are associated with this profile at p < 0.05?
    • 152
  6. How many GO terms are associated with this profile with a corrected p value < 0.05?
    • 92
  7. 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?
    • ribosome biogenesis - A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis. [1]
    • preribosome - Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis. [2]
    • nuclear lumen - The volume enclosed by the nuclear inner membrane. [3]
    • cellular component biogenesis - A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. [4]
    • maturation of SSU-rRNA - Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule. [5]
    • cleavage involved in rRNA processing - Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. [6]
    • RNA phosphodiester bond hydrolysis - The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis. [7]
    • intracellular non-membrane-bounded organelle - Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. [8]
    • nucleobase-containing compound metabolic process - Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. [9]
    • cellular aromatic compound metabolic process - The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. [10]
    • In the gene profile I have chosen to look at, the genes were up regulated after cold shock, and then the levels were down regulated during recovery. Looking at all the GO terms, the genes in this profile make sense. The majority of these have to deal with cell organelle biogenesis, membrane regulation, and RNA processing. During cold shock, the cells would need to build new proteins to deal with the cold. They also have to maintain the fluidity of their membrane for survival, so an up regulation of these proteins would be needs. Ribosomes are directly involved with protein synthesis, and since the cells is trying to build cold shock response proteins, there would need to be more production of ribosomes, which many of the genes in this cluster are responsible for.

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 - 29.5%
    • Rap1p - 23.5%
    • Sko1p - 16.4%
    • Sok2p - 15.7%
    • Ino4p - 14.6%
    • Yap6p - 12.8%
    • Cin5p - 12.1%
    • Skn7p - 11.7%
    • Phd1p - 10.0%
    • Abf1p - 10.0%
  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 regulates 12.1% of the genes, which is 34 genes.
    • Gln3 regulates 2.1% of the genes, which is 6 genes.
    • Hmo1 does not regulated any of these genes listed.
    • Zap1 regulates 0.4% of the genes, which is 1 gene.
  3. Which transcription factors do you want to add to the model and why?
    • I would like to add Ste12, Rap1, and Sok2 to the list because for this cluster of genes, which is the most significant in all of our data, these are three of the top transcription factors that regulate the most number of genes. They also regulate many of the same genes in this cluster.

Uploaded Files


STEM Profile Powerpoint


Gene Image

Excel Matrix

Regulation Matrix

Useful Links