ermineJ: GO enrichment analysis

ermineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. Read more at http://erminej.chibi.ubc.ca/

Input files:

  • GO xml file (download here);
  • Annotation file (TAB delimited):
    GeneID<TAB>GeneID<TAB>Description<TAB>GO:0016020,GO:0008519…
    If more than one GO term is associated to a gene, it should be separated by commas.
  • Gene score file (TAB delimited):
    GeneID<TAB>Score

Installation

For linux users, download the “Generic bundle” version and unzip the file on your home directory. Rename the folder “ermineJ-3…*”  to “ermineJ”.

ErmineJ requires you to set some global variables on the file “bash.bashrc”. For this, first you need to find out where is installed your Java. Type on shell:

$which java

You’ll probably get a message like this: /usr/bin/java. This is the path that will be defined to the global variable JAVA_HOME. Now, let’s edit the file bash.bashrc to set the variables:

$sudo vim /etc/bash.bashrc

Add the following lines to the end of the file:

JAVA_HOME=/usr/bin/java
export JAVA_HOME
PATH=$PATH:$JAVA_HOME
export PATH
export ERMINEJ_HOME=/home/ermineJ

Close and save the changes: Esc + : + wq + Enter

And reload:

$source /etc/bash.bashrc

 

Executing ermineJ

Navigate to directory /home/ermineJ/bin/ and give permission to execute the file ermineJ.sh:

$sudo chmod 777 ermineJ.sh

then, type this a minimal command line to run the ermineJ:

$./ermineJ.sh -s geneScores.txt -c ~/ermineJ.data/go_daily-termdb.rdf-xml.gz -a annotationfile.txt -n ORA -t 0.001 -x 100 -y 10 -j > results.txt

-s [Gene scores file]
-c [GO xml file] download here
-a [Annotation file] -n [Method for computing gene set significance]
-t [Threshold value; default = 0.001]
-x [Sets the maximum class size; default = 100]
-y [Sets the minimum class size; default = 10]
-j [Output should include gene symbols for all gene sets]

For more control options type:

$./ermineJ.sh

If you still get any error message, try to change the line 78 from the ‘ermineJ.sh’ file as following:

JAVACMD=”$JAVA_HOME/bin/java”

to

JAVACMD=”$JAVA_HOME”

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