GESS

Uploading an si/shRNA file:

The program accepts comma or tab separated text files or Excel files.

Input file containing active and inactive si/shRNAs:	Example si/shRNA File 1	This file should have at least three columns; first column with siRNA identifiers that can be any number given by the user, second column with si/shRNA sequences and third column with phenotype/activity data.
Input file containing only active si/shRNAs:	Example si/shRNA File 2	This file should have at least two columns; first column with si/shRNA identifiers that can be any number given by the user and second column with si/shRNA sequences.

Uploading a custom database file:

All transcript sequences must be in FASTA format in this file.

Custom database file:

Custom Database File Example

If the user wants to provide a custom database file, it should contain FASTA formatted sequences. The information written on the comment line (after ">") will be used as sequence identifier.

Resulting Files:

File with GESS analysis results:	Example Gess Results File 1	This file contains basic GESS analysis output. Analysis results for each tested sequence is listed in a tab delimited format. See the help page for more information.
File with tested sequences and matching "active" si/shRNAs:	Example Gess Results File 2	This file lists tested sequences with matching "active" si/shRNAs to them. Note that only significant transcripts (p value cut-off 0.05) are listed here and they are NOT sorted.