Transcript Norwich_tom_heather_hinkle

Experimental summary
Norwich DMSO treated versus
Control Yeast
Tom Smith, Heather St. Martin,
Karen Hinkle
• 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
– P-value: not significant (p > 0.005)
•
Gene YHB1 had the following F.C and p-value in DMSO treated versus
control
– Fold change: 1.4-fold decrease in expression
– P-value: not significant (p > 0.005)
Were your genes in the final Set of
Selected Genes?
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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
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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