Functional pathway response analysis and application to gene expression in papilloma of p27 mutant mice

Download R code and gene expression data

R code and data set

FuncPathResp-p27_0.0.1.zip (Download size ~753 KB)

1.     The p27 gene expression data is saved in the file “data/expression.txt”

2.     The “data/” folder also contains gene sets associated with mouse pathways downloaded from KEGG

3.     The source code is provided in six R source code files within “code/”

4.     A “results/” folder contains all output files after running the R code

 

Installation requirement

1.     Must install R project

2.     The software requires several R packages. If not present, they will be automatically installed. Depending how R is installed, package installation may not succeed if the user does not have sufficient privilege. Contact your system administrator if this happens

3.     Unzip the compressed file and maintain the directory organization

 

Running the software

1.     Start R within the top level of the unpacked directory

2.     Type in the following command in R:

> source(“./code/Main.R”)

3.     Choose the three options on the menu to run the program for single gene analysis, pathway response analysis by full permutation test (slow), and pathway response analysis by gamma approximation

4.     The results can be found in the “results/” folder

 

How to cite the work

Nguyen, H. H., S. C. Tilton, C. J. Kemp, and M. Song. Non-monotonic gene expression response to Cdkn1b dosage suggests oncogenic role of p27/Kip1 at intermediate dose.  (Submitted)

 

License

Free to academic institutions. Commercial organizations need to contact the maintainer to obtain an appropriate license.

 

Copyright

Copyright © 2015 New Mexico State University