We did whole transcriptome sequencing (RNAseq) of 6 samples (3 normal vs. 3 tumor) and ended with 270 differentially expressed genes : 200 up regulated and 70 down regulated. I want to use ToppGene for Candidate gene prioritization of our 270 genes, I know that sounds stupid but I couldn't find any proper manual of toppgene written in plain English and I'm very confused on how to use this software.
Here is the link: https://toppgene.cchmc.org/prioritization.jsp
It has 2 blanks to fill, "training gene set" and "test gene set" and don't understand what should I fill out in there. Let's say, if I need to do Candidate gene prioritization of our up regulated gene set (200) what should go in training and test gene set?
1 answer
Here's the link to the help file, in case, you haven't found it yet: https://toppgene.cchmc.org/help/help.jsp
From what you have stated, you can either use all 270 as the test set or do it separately (200 upregulated and 70 downregulated). I would recommend doing separately so that you will have ranked down and up candidates. You need training set though. Typically training set should be established prior knowledge (known genes associated/related to phenotype of your interest or pathway, etc.).
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