Gene Category Enrichment using Mann-Whitney U tests
Download MWU.zip to personal computer to for demo R scripts and datasets.
Exercises:
Unzip MWU.zip on personal computer.
The MWU directory three subdirectories:
exercise1_fisher_test
exercise2_go_mwu
exercise3_kog_mwu
- Example enrichment analysis using Fisher's Exact test
- open exercise1_fisher_test
- open the R script 'example_fisher_test.R'
- set the working directory as the path to 'exercise1_fisher_test/'
- execute the commands in the script to see if the fake GO term 'schmooase' is enriched among the differentially expressed genes.
- GO Mann-Whitney U Enrichment test
- open exercise2_go_mwu
- open the R script 'GO_MWU.R'
- set working directory as the path to 'exercise2_go_mwu/'
- execute the commands to build a dendrogram of enriched Cellular Component GO terms
- Edit the script to assign the goDivision variable to look at Molecular Function instead of Cellular Component
- Re-execute all the commands to build the dendrogram for Molecular Function GO terms
- kog Mann-Whitney U Enrichment analysis
- open KOG_MWU_heat.R
- set working directory
- use bioconductor to install the package
- execute the commands
- What do the results suggest about transcriptional response to heat stress in adult and larval corals?
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