Download Norwich_Cyle

Experimental summary
Norwich DMSO treated versus
Control Yeast
Cyle A. Davenport
• My hypothesis is that the genes PPH21,
CTS1, and CDC40 will be up regulated or
down regulated in the DMSO sample versus
control
• I base this hypothesis on the fact that these
genes are known to be involved in mitosis
• This information was obtained from
www.yeastgenome.org
Gene ontology
• My gene PPH21 has been assigned the following GO
categories: protein phosphatase 2A, G1/S transition of
mitotic cell cycle, budding cell growth
• My gene CTS1 has been assigned the following GO
categories: endochitinase activity, cytokinesis
• My gene CDC40 has been assigned the following GO
categories: Nucleic acid binding, pre-splicing of mRNA,
DNA replication, S phase of mitosis
Detection call summary
• Gene PPH21 had the following detection calls in the
experiment: Present in all eight samples, not significant
• Gene CTS1 had the following detection calls in the
experiment: Present in all eight samples, not significant
• Gene CDC40 had the following detection calls in the
experiment: Present in all eight samples, p-value<0.005
Fold change and p-values
• Gene PPH21 had the following F.C and p-value in
DMSO treated versus control: FC-1.16, p-value>0.005
• Gene CTS1 had the following F.C and p-value in DMSO
treated versus control: FC-1.18, p-value>0.005
• Gene CDC40 had the following F.C and p-value in
DMSO treated versus control: FC-1.86, p-value-0.003
Were your genes in the final Set of
Selected Genes?
•
•
•
•
Gene PPH21 - NO
Gene CTS1 - NO
Gene CDC40 - YES
The first two genes were not in the final set because
their p-values were not small enough. Therefore these
genes did not fluctuate as much as I thought they would
Making Inferences
• The following common interacting pathways exhibited
differential gene expression: mRNA processing and
mitotic cell cycle
Making Inferences
• Evidence for this pathway’s disregulation is further
reinforced by the following data mined from public data
bases
Experimental conclusion
•
•
The gene CDC40 I anticipated to be disregulated with the treatment of
DMSO were confirmed by the data analysis and reinforced by additional
data in the public realm leading me to conclude that DMSO has some
effect on mRNA processing and the mitotic cell cycle of yeast.
The genes PPH21 and CTS1 I anticipated to be disregulated with the
treatment of DMSO were not confirmed by our experimental data
–
1.
2.
3.
Three reasons that could have lead to the non-confirmed result
DMSO does not disrupt budding cell growth
DMSO does not disrupt cytokinesis
DMSO does not disrupt chitin catabolism
I am now an official UVM microarray data analyst
and the results of my analysis are posted here