KEA
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KEA command line version

Download Files

Here you can download all files needed to run KEA as a command line desktop application and KEA windows installer. If using the KEA installer follow the instructions of the install wizard and read the "readme.txt" in the installation directory. "kea.jar" is the command line version of KEA, "background.csv" contains all kinase-substrate relations that are also used in the web application of KEA. "genelist.csv" is a randomly generated list of genes/proteins. We also support BioPAX an OWL/XML and our own sig flat-file format.
| kea-windows-installer.exe (contains all needed data files) | kea.zip (all files) | kea.jar | background.csv | genelist.csv |
OWL format: keaowl.zip
Sig format: keasig.zip

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.

KEA GUI

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

Here you can download all files needed to run KEA as a command line desktop application and KEA windows installer. If using the KEA installer follow the instructions of the install wizard and read the "readme.txt" in the installation directory. "kea.jar" is the command line version of KEA, "background.csv" contains all kinase-substrate relations that are also used in the web application of KEA. "genelist.csv" is a randomly generated list of genes/proteins. We also support BioPAX an OWL/XML and our own sig flat-file format.
| kea-windows-installer.exe (contains all needed data files) | kea.zip (all files) | kea.jar | background.csv | genelist.csv |
OWL format: keaowl.zip
Sig format: keasig.zip
| Ma'ayan Laboratory | Systems Biology Center New York | Mount Sinai School of Medicine |
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Please cite, Lachmann A, Ma'ayan A. KEA: Kinase Enrichment Analysis.Bioinformatics. 2009 Jan 28.