KEA command line version
Download Files
Please register to our website once to download the supporting files. You are free to use the provided sources for academic purposes.
GUI
If you choose to run KEA as a desktop application just double click on the
kea.jar file. If the jar is executed without any parameters a small GUI interface will pop up. It will ask you for some input information in order to run the analysis. A picture of the interface is shown below. Choose a gene list to analyze as well as a background database containing the kinase-substrate relations.
Then choose a name for the output file and the level for the analysis. By pressing the
Start KEA button the computation is initiated. The menu will return to its initial state once the computation is complete. For specifications of the input file formats please read the sections below and refer to the files in the download section.
Running from the Command Line
The command line version can be useful in combination with other scripts to analyze multiple files of gene lists. If the
kea.jar is started with the needed parameters it will run as command line app.
In order to use the KEA program you need a background database file. Each line of the background data file contains 4 entries. The first is a kinase class,
the second a kinase family, third a kinase and at the end the target of the kinase. As an example the file should look like:
...
AGC,AKT,AKT1,CREB1
CMGC,CDK,CDC2,MAP2
STE,STE20,PAK7,RAC1
...
A background data file can be downloaded from
here. It is the same database that is used for the web version of KEA.
Additionally you need a file that contains a list of genes that will be used to compute the enrichment for the kinases. In order for the program to work correctly the genes should be encoded with the same ID as in the background file.
The background file provided uses
Entrez Gene Symbols. Each line of the file should contain one gene. As an example, the file should look like this:
...
SUPV3L1
TBC1D22A
TCEA1
TUBB6
UBP1
UTP11L
WBP7
YLPM1
...
An example gene list can be downloaded from
here.
The command line version of KEA is implemented in JAVA and was tested with JAVA 1.6. To run the
kea.jar 4 parameters are expected. First the name of the background database, second the gene-list, third the name of the output file and finally an integer defining the level of analysis.
The levels of analysis are
kinase-class,
kinase-family and
kinase. The integers representing these levels are:
0 = kinase-class
1 = kinase-family
2 = kinase
If for example integer 1 is chosen, the enrichment computation for kinase families will be performed.
To run the program enter on the command line the following:
c:\path of jar file>kea.jar background.csv genelist.csv keaoutput.csv 1
KEA will generate an output file with the name specified as the third parameter. In the example, the results will be outputted to a file named keaoutput.csv.
Each line in this file contains information about the kinase-class, kinase-family or kinase (depending on the analysis level).
Eight values are generated, separated by a comma:
1. name of kinase-class, kinase-family or kinase
2. number of substrates that are phosphorylated by the kinase-class, kinase-family or kinase
3. the fraction of substrates targeted compared to total number of substrates in background
4. number of targets in the input gene-list
5. the fraction of substrates targeted compared to total number of substrates in gene-list
6. difference between the background fraction and the gene-list fraction
7. p-value computed using the Fisher Test
8. list of substrates separated by a semi-colon
If you should have any questions concerning KEA please
contact us.
Download Files
Please register to our website once to download the supporting files. You are free to use the provided sources for academic purposes.
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