1. Experimental summary Norwich DMSO treated versus Control Yeast
Tom Smith, Heather St. Martin, Karen Hinkle

2. I base this hypothesis on the following information:
Our hypothesis is that the gene FIG1 will be downregulated and the genes BDH1 and YHB1 will be up regulated in the DMSO sample versus control
I base this hypothesis on the following information:
FIG1: This gene is involved is required for sufficient mating
BDH1: This gene is involved during aerobic growth and during environmental stress it was upregulated
YHB1: This gene is upregulated in response to environmental stress
This information was obtained from the following sources (

3. Gene ontology My gene has been assigned the following GO categories
FIG1
Molecular function: unknown
Biological function: involved in shmoo formation
Subcellular localization: cell wall
BDH1
Molecular function: (R,R)-butanediol dehydrogenase activity
Biological function: butanediol fermentation
Subcellular localization: cytoplasm
YHB1
Molecular function: nitric oxide reductase activity
Biological function: response to stress
Subcellular localization: cytoplasm, cytosol

4. Detection call summary
Gene FIG1 had the following detection calls in the experiment (Present in all samples, T1-T8)
Gene BDH1 had the following detection calls in the experiment (Present in all samples, T1-T8)
Gene YHB1 had the following detection calls in the experiment (Present in all samples, T1-T8)

5. Fold change and p-values
Gene FIG1 had the following F.C and p-value in DMSO treated versus control
Fold change: 1.5-fold increase in expression
P-value: not significant (p > 0.005)
Gene BDH1 had the following F.C and p-value in DMSO treated versus control
Fold change: 1.3-fold decrease in expression
Gene YHB1 had the following F.C and p-value in DMSO treated versus control
Fold change: 1.4-fold decrease in expression

6. Were your genes in the final Set of Selected Genes?
Gene FIG1: No
Gene BDH1: No
Gene YHB1: No
While all three genes were present in all samples, none of the three made passed the p-value criterion

7. Making Inferences
Since our genes did not show significant changes in DMSO-treated samples, we focused on another pathway that was changed
The following common interacting pathways exhibited differential gene expression: histone regulation/acetylation related to transcriptional silencing
Evidence for this pathway’s disregulation is shown by the following visualizations: Significant upregulation of 12 genes involved in transcriptional silencing due to histone modification (SAS3, SNT1, SIR2, SIR4, HDA2, TAF1, SET3, BRE2, SIR3, SAS2, SPP1, HPA2)

8. Making Inferences
Evidence for this pathway’s disregulation is further reinforced by the following data mined from public data bases
TAF1 was significantly upregulated in another microarray dataset (Expression in response to environmental changes) in which yeast were exposed to stressful conditions
Source: Expression Connection in

9. Experimental conclusion
TAF1, along with other genes involved in histone modifyification and transcriptional silencing, was upregulated in the DMSO condition
The genes FIG1, BDH1, and YHBI we anticipated to be disregulated with the treatment of DMSO were not confirmed by our experimental data
Three reasons that could have lead to the non-confirmed result
The p-value criterion was too stringent to pick up more subtle changes in gene expression
DMSO treatment does not affect shmooing processes or aerobic growth pathways
There may be other unknown biological functions attributed to the genes we focused on that may explain why these genes were unchanged

10. I am now an official UVM microarray data analyst and the results of my analysis are posted here