AutoCompare ZE
AutoCompare_ZE is a software which scores the enrichment of a gene set in a gene list.
AutoCompare_ZE is based on the Zelen’s exact test. We demonstrated that this test solves the false discovery problem observed with the Fisher's exact test.
Citation :
When using AutoCompare_ZE to process data for publication please cite:
Curbing false discovery rates in interpretation of genome-wide expression profiles. Ycart B, Pont F, Fournié JJ. J Biomed Inform. 2014 Feb;47:58-61.
AutoCompare ZE interface
Example of results Table : FE : Pvalue with the classical Fisher Exact test, ZE : Pvalue with the Zelen’s exact test.
Manual :
AutoCompare ZE is a GNU Linux/Unix multithread software.
1- if not already installed, install Perl free programming language
2- install R programming language.
4- Install Tk
5- unzip the software
6- copy your lists of gene names in the data directory
7- copy your databases in the databases directory. Databases are text files, each file contains a list of gene and the title of the file is name of the biological function. The files should be placed in a directory and the name of the directory is the name of the database.
8- open a terminal. In the AutoCompare-ZE dirctory type : perl AutoCompareZE_DBlink_0.3.pl to start the software.
9- choose your databases and the number of CPUs and press the "start" button.
10- processed files are in the “results” directory.
Here we provide databases of > 20 000 biological functions, pathways etc... We also provide random samples and random databases to establish score thresholds.
TIP
It is possible to use AutoCompareZE without graphical interface and without the need to install perl/Tk which is tricky on windows.
1- you can try this version AutoCompare ZE cmdline
2- you can alternatively edit the file automatic_compare_confZE.txt and then start the sofware with the command : perl ZE_process.pl