Difference between revisions of "Ymesfin Week 9"
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==Methods== | ==Methods== | ||
| − | + | #The data was first downloaded from the wiki | |
| − | *Why did you select this profile? In other words, why was it interesting to you? | + | #*The strain we will be analyzing is Delta-Hap4 |
| − | **I chose Profile 48 because it was the third most significant profile and the expression of the gene appeared parabolic. | + | #*The data was obtained from the following file: [[Media: Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx| Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx]] |
| − | *How many genes belong to this profile? | + | #*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. |
| − | **256 genes are associated with this profile. | + | #Performed ANOVA Statistical Analysis |
| − | *How many genes were expected to belong to this profile? | + | ##Calculated average results for each datapoint. |
| − | **32.6 genes were expected to be associated with this profile. | + | ##Calculated Sum square of the entire dataset |
| − | *What is the p-value for the enrichment of genes in this profile? | + | ##Created the column headers dHAP4_ss_(TIME) for each timepoint. |
| − | **The p-value of enrichment for this profile is 1.8E-141 | + | ##Calculated Sum Square for each timepoint |
| − | *How many GO terms are associated with this profile at p < 0.05? | + | ##Calculated Fstat for each data point |
| − | **35 terms associated with this profile have a p-value < 0.05. | + | ##Calculated p value for each data point |
| − | *How many GO terms are associated with this profile with a corrected p value < 0.05? | + | ##Perfomed Bonferroni p value correction for each data point |
| − | **Only one term associated with this profile had a corrected p value < 0.05. | + | ##Performed Benjamini & Hochberg p value Correction for each data point |
| + | ##Performed Sanity check | ||
| + | #Clustering and GO Term Enrichment with STEM Software | ||
| + | ##The data was copied onto a new excel sheet | ||
| + | ##Column A was renamed to "SPOT", Column B was renamed "Gene Symbol", and the column named Column C was deleted | ||
| + | ##All the data entries with BH p-values > 0.05 were deleted | ||
| + | ##All of the data columns except for the Average Log Fold change columns for each timepoint were deleted | ||
| + | ##The data columns were renamed with just the time and units (for example, 15m, 30m, etc.) | ||
| + | ##The data was saved as a tab-delimited text document | ||
| + | ##The STEM Software, Gene Ontology, and yeast GO annotations were downloaded | ||
| + | ##The STEM Software was run using the dHAP4 text data | ||
| + | ##The Profile GO and Profile Gene Tables were saved from the STEM results | ||
| + | ##Profile 48 from the STEM results was selected for further analysis | ||
| + | ##*Why did you select this profile? In other words, why was it interesting to you? | ||
| + | ##**I chose Profile 48 because it was the third most significant profile and the expression of the gene appeared parabolic. | ||
| + | ##*How many genes belong to this profile? | ||
| + | ##**256 genes are associated with this profile. | ||
| + | ##*How many genes were expected to belong to this profile? | ||
| + | ##**32.6 genes were expected to be associated with this profile. | ||
| + | ##*What is the p-value for the enrichment of genes in this profile? | ||
| + | ##**The p-value of enrichment for this profile is 1.8E-141 | ||
| + | ##*How many GO terms are associated with this profile at p < 0.05? | ||
| + | ##**35 terms associated with this profile have a p-value < 0.05. | ||
| + | ##*How many GO terms are associated with this profile with a corrected p value < 0.05? | ||
| + | ##**Only one term associated with this profile had a corrected p value < 0.05. | ||
| + | ##The definitions of the top 6 terms with p-values <0.05 were searched on http://geneontology.org | ||
==Results== | ==Results== | ||
Revision as of 15:30, 26 October 2019
Contents
Purpose
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
- Calculated average results for each datapoint.
- Calculated Sum square of the entire dataset
- Created the column headers dHAP4_ss_(TIME) for each timepoint.
- Calculated Sum Square for each timepoint
- Calculated Fstat for each data point
- Calculated p value for each data point
- Perfomed Bonferroni p value correction for each data point
- Performed Benjamini & Hochberg p value Correction for each data point
- Performed Sanity check
- Clustering and GO Term Enrichment with STEM Software
- The data was copied onto a new excel sheet
- Column A was renamed to "SPOT", Column B was renamed "Gene Symbol", and the column named Column C was deleted
- All the data entries with BH p-values > 0.05 were deleted
- All of the data columns except for the Average Log Fold change columns for each timepoint were deleted
- The data columns were renamed with just the time and units (for example, 15m, 30m, etc.)
- The data was saved as a tab-delimited text document
- The STEM Software, Gene Ontology, and yeast GO annotations were downloaded
- The STEM Software was run using the dHAP4 text data
- The Profile GO and Profile Gene Tables were saved from the STEM results
- Profile 48 from the STEM results was selected for further analysis
- Why did you select this profile? In other words, why was it interesting to you?
- I chose Profile 48 because it was the third most significant profile and the expression of the gene appeared parabolic.
- How many genes belong to this profile?
- 256 genes are associated with this profile.
- How many genes were expected to belong to this profile?
- 32.6 genes were expected to be associated with this profile.
- What is the p-value for the enrichment of genes in this profile?
- The p-value of enrichment for this profile is 1.8E-141
- How many GO terms are associated with this profile at p < 0.05?
- 35 terms associated with this profile have a p-value < 0.05.
- How many GO terms are associated with this profile with a corrected p value < 0.05?
- Only one term associated with this profile had a corrected p value < 0.05.
- Why did you select this profile? In other words, why was it interesting to you?
- The definitions of the top 6 terms with p-values <0.05 were searched on http://geneontology.org
Results
Data and Files
dHAP4 P-Values and Stem Results
