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GEMOT: GEnetic and MOlecular mechanisms of connections among Traits.

 

Using GEMOT on the website

 

A version of GEMOT application is freely available on different browsers including FireFox version 22 (22.0 and higher),
Chrome version 28 (28.0.1500.72 and higher), Safari version 6 (6.0.2 and higher) and Explorer version 10 (10.0.9200 and higher).

Users interested in commercial applications should contact Dr. Irit Gat-Viks.

 

GEMOT manual

The GEMOT manual is available here. The manual provides instructions on how to apply the GEMOT analysis.

 

Example files

GEMOT takes the following inputs:

1.      A molecular data (e.g., gene expression) file.

2.      A trait measurements file.

3.      A genotyping file.

4.      An index file for molecular components (e.g., genes).

5.      An index file for traits.

6.      An index file for genetic variants.

7.      A run parameters file.

8.      Association scores file (optional for inbred strains).

All these inputs should be uploaded by the user. In addition, GEMOT takes command line parameters that are detailed in the manual.

GEMOT provides the following outputs:

  1. A module summary file.
  2. Modules' traits file.
  3. Modules' genes file.

 

Additional explanations about the input and output file format and pre-processing are in the manual. Example files are available here, and detailed in the manual.

 

Running GEMOT

To run the GEMOT algorithm, proceed as follows:

  1. Prepare all input files and update the run-parameters file accordingly. The names of the output file names should also be specified in the run-parameters file. The run-parameters file should be called "run-parameters.txt"
  2. Put all the input files, including the run-parameters file in a certain directory (e.g. "my_dir").
  3. Use the following three commands sequentially:
    > java -jar -Xmx4096m GEMOT.jar 0 my_dir > log.txt

The people behind GEMOT

GEMOT was developed in:
Dr. Irit Gat-Viks's System Genetics Laboratory at the Cell Research and Immunology Department,
Faculty of Life Sciences, Tel Aviv University, Israel;

 

References

[1] Yael Oren, Aharon Nachshon, Amit Frishberg, Roni Wilentzik, Irit Gat-Viks. Dissecting dynamic genetic variation controlling temporal gene response in yeast. Elife. 2015;4

 

Feedback

For any questions, bugs and suggestions please contact: Yael Oren.

 

Copyright information

Copyrights Tel-Aviv University, Israel (2013).

 

The name of contributors may be used to endorse or promote products derived from this software without specific prior written permission.

This software is provided "AS IS," without a warranty of any kind. ALL EXPRESS OR IMPLIED CONDITIONS,
REPRESENTATIONS AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED.

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