Ymesfin Week 8

Purpose

The purpose of this assignment was to create a detailed electronic lab notebook to statistically analyze a DNA microarray dataset and to demonstrate our understanding of p-value cut-offs.

Week 7 Assignment

Week 8 Assignment

Methods

The data was first downloaded from the wiki
- The strain we will be analyzing is Delta-Hap4
- The data was obtained from the following file: Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx
- The file had timepoints at 15, 30, 60, 90, and 120 minutes. All the timepoints had 4 replicates but the 90 and 120 minute timepoints had 3 replicates. There were a total of 6189 samples in this dataset.
Performed ANOVA Statistical Analysis
1. Calculated average results for each datapoint.
2. Calculated Sum square of the entire dataset
3. Created the column headers dHAP4_ss_(TIME) for each timepoint.
4. Calculated Sum Square for each timepoint
5. Calculated Fstat for each data point
6. Calculated p value for each data point
7. Perfomed Bonferroni p value correction for each data point
8. Performed Benjamini & Hochberg p value Correction for each data point
9. Performed Sanity check
Clustering and GO Term Enrichment with STEM Software

Results

Files

dHAP4 Data Sheet

dHAP4 stem data

P Values and Stem Results

Conclusion

In this study, yeast cells (saccharomyces cerevisiae) were exposed to a cold shock to monitor how their gene expression levels related to environmental temperatures. The ANOVA suggest that approximately 40.1% of the collected data is statistically significant and had p values less than 0.05. However, given the large number of data entries used in the study, it is not unreasonable to assume that some of the significant results are due to chance, regardless of whether the p values were less than 0.05. Nonetheless, 4.5% of the data contained p values less than 0.0001, substantiating the significance of at least some of the data. Thus, the database suggests that there is a relationship between the expression levels of certain genes of saccharomyces cerevisiae and the cold shock treatments.