Individual Journal Week 12

Analyzing and Interpreting STEM Results

• Why did you select this profile?
  • I selected profile 45 because for the first 3 times, it had a pattern of upregulation. The t120 time is clearly downregulated, suggesting a possible response to cold-shock that changes at t120.
• How many genes belong to this profile?
  • 388
• How many genes were expected to belong to this profile?
  • 46.9
• What is the p value for the enrichment of genes in this profile?
  • p=2.3E-224
• How many GO terms are associated with this profile at p<0.05?
  • 165
• How many GO terms are associated with this profile with a corrected p value <0.05?
  • 35
• 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:0008186-RNA-dependent ATPase activity: Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
  • GO:0034661-ncRNA catabolic process: The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs).
  • GO:0006400-tRNA modification: The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • GO:0019843-rRNA binding: Interacting selectively and non-covalently with ribosomal RNA.
  • GO:0043634-polyadenylation-dependent ncRNA catabolic process: The chemical reactions and pathways resulting in the breakdown of a noncoding RNA (ncRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target ncRNA.
  • GO:0071029-nuclear ncRNA surveillance: The set of processes involved in identifying and degrading defective or aberrant ncRNAs within the nucleus.
  • GO:0071046-nuclear polyadenylation-dependent ncRNA catabolic process: The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of primarily noncoding RNA (ncRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target ncRNA
  • GO:0000467-exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA: Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.
  • GO:0004004-ATP-dependent RNA helicase activity:Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
  • GO:0000054-ribosomal subunit export from nucleus: The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
• The majority of these functions deal with the degradation and modification of RNA. I am struggling to figure out how to differentiate between up-regulated and down-regulated genes based on geneontology website or the data given, but considering that the t15, t30, t60, t90 are up-regulated, while only t-120 is down-regulated, it would probably be reasonable to assume that these functions are mostly up-regulated. This would mean that due to cold-shock, cells primarily increase the breakdown of RNA,and mores specifically non-coding RNA, as suggested by the GO terms. This suggests that cold-shock induces translation in order to produce specific proteins involved in stress response.

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

• What are the top 10 transcription factors in your results?
  • Ste12: 29.4%
  • Rap1: 20.8%
  • Sko1: 14.8%
  • Ino4: 14.5%
  • Sok2: 13.2%
  • Yap6: 10.4%
  • Fhl1: 9.9%
  • Abf1: 9.9%
  • Tec1: 9.9%
  • Reb1: 9.1%
• Are Cin5, Gln3, Hmo1, and Zap1 on the list? What percentage of the genes in the cluster do they each regulate? How many genes do they each regulate?
  • Cin5: 9.1%, 36 genes
  • Gln3: 2.6%, 10 genes
  • Hmo1: not on list
  • Zap1: 1.0%, 4 genes
• Which transcription factors do you want to add to the model and why?
  • Ste12,Rap1, Ino4 are the transcription factors with the highest percentages that are not on the list and that regulate the most amount of genes. Also these transcription factors regulate many of the same genes. Thus, I would add them to the model.

STEM & YEASTRACT Powerpoint

File:STEM and YEASTRACT.pptx

Regulation Matrix

File:Regulation Matrix.xlsx