Experimental summary Norwich DMSO treated versus Control Yeast

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Presentation transcript:

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

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 (www.yeastgenome.org)

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

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)

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

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

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)

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 www.yeastgenome.org

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

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