/
Gene Category Enrichment using Mann-Whitney U tests

Gene Category Enrichment using Mann-Whitney U tests

May 26, 2016

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

 

  1. Example enrichment analysis using Fisher's Exact test

    1. open exercise1_fisher_test

    2. open the R script 'example_fisher_test.R'

    3. set the working directory as the path to 'exercise1_fisher_test/'

    4. execute the commands in the script to see if the fake GO term 'schmooase' is enriched among the differentially expressed genes.

  2. GO Mann-Whitney U Enrichment test

    1. open exercise2_go_mwu

    2. open the R script 'GO_MWU.R'

    3. set working directory as the path to 'exercise2_go_mwu/'

    4. execute the commands to build a dendrogram of enriched Cellular Component GO terms

    5. Edit the script to assign the goDivision variable to look at Molecular Function instead of Cellular Component

    6. Re-execute all the commands to build the dendrogram for Molecular Function GO terms

  3. kog Mann-Whitney U Enrichment analysis

    1. open KOG_MWU_heat.R

    2. set working directory

    3. use bioconductor to install the package

    4. execute the commands

    5. What do the results suggest about transcriptional response to heat stress in adult and larval corals?