CHEA
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Download the manual database and the command-line enrichment analysis tool

CHEA command line version

Download Files

Here you can download all files needed to run CHEA as a command line desktop application and CHEA windows installer. If using the CHEA installer follow the instructions of the install wizard and read the "readme.txt" in the installation directory. "CHEA.jar" is the command line version of CHEA, "chea-background.zip" contains all transcription factor target data that are also used in the web application of CHEA. "genelist.csv" is a randomly generated list of genes/proteins.
| chea-windows-installer.exe (contains all needed data files) | chea.zip (all files) | chea.jar | chea-background.zip | genelist.csv |

GUI

If you choose to run CHEA as a desktop application just double click on the CHEA.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 transcription factor - target relations. Then choose a name for the output file for the analysis. By pressing the Start CHEA 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.

CHEA 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 chea.jar is started with the needed parameters it will run as command line app. In order to use the CHEA program you need a background database file. Each line of the background data file contains 3 entries. The first is a transcription factor and pubmed id, the second a reported transcription factor target, third th pubmed id from the publication the interaction was reported. As an example the file should look like:
...
ZFP42-18358816,ZFP346,18358816
POU5F1-18692474,RANBP1,18692474
NANOG-18358816,4930583K01RIK,18358816
...
A background data file can be downloaded from here. It is the same database that is used for the web version of CHEA.

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 CHEA is implemented in JAVA and was tested with JAVA 1.6. To run the chea.jar 3 parameters are expected. First the name of the background database, second the gene-list and third the name of the output file of analysis. To run the program enter on the command line the following:
c:\path of jar file>chea.jar chea-background.csv genelist.csv cheaoutput.csv

CHEA 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 cheaoutput.csv. Each line in this file contains information about a transcription factor. Eight values are generated, separated by a comma:
1. name of the transcription factor
2. number of genes that are targeted by the transcription factor
3. the fraction of genes targeted compared to total number of genes in background
4. number of targets in the input gene-list
5. the fraction of genes targeted compared to total number of genes 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 genes separated by a semi-colon
If you should have any questions concerning CHEA please contact us.

Download Files

Here you can download all files needed to run CHEA as a command line desktop application and CHEA windows installer. If using the CHEA installer follow the instructions of the install wizard and read the "readme.txt" in the installation directory. "CHEA.jar" is the command line version of CHEA, "chea-background.zip" contains all transcription factor target data that are also used in the web application of CHEA. "genelist.csv" is a randomly generated list of genes/proteins.
| chea-windows-installer.exe (contains all needed data files) | chea.zip (all files) | chea.jar | chea-background.zip | genelist.csv |
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