EPEE outputs interpretation

[JamalEH]

Dear EPEE team,

First of all, thank you so much for the great tool, EPEE.

I recently run EPEE tool on my gene expression data from RNA-Seq (2conditions/3 replicates each) and using an appropriate TF-gene network model from FANTOM5, as stated in the README part. I got 4 different output files after 20 different runs of EPEE and I need your help to understand the output files. The 4 separate files I got are listed as follows ::

1. all_perturb_scores.txt
2. all_regulator_scores.txt
3. perturb_scores.txt
4. regulator_scores.txt

As far as I understood the perturb scores files refer to the genes being differentially regulated between my two conditions and regulator scores files refer to differentially regulated TF between my two conditions. Now how should I read this files? Does the given scores for perturbed genes represents in some way the significance of perturbation? Is there any cut-off that the scores should fulfil to consider the gene is being significantly perturbed between the two conditions? The same questions are also for the regulators.

I will be grateful if if you can help me interpret the results so I can pick-up the most significant perturbations for further investigations.

Thank you so much in advance!
PS: I used exactly the same command line stated on the code page with the following options -r 20 -w -mp -p .
Best regards,
Jamal.

[virenar]

Sorry for late response. Would be really interested to know if you received any meaningful results.

Regarding the scores, these are log likelihood scores described in the Supplementary Methods section 1.1 & 1.2. They don't represent significance of perturbation. You can do permutation testing described in section 1.3 to obtain significance of these scores. Hope that helps.

Lets us know if you have any additional questions.