Differential binding for genotype-treatment interaction

[ikumar2000]

Is it possible to run a genotype-treatment interaction type analysis for differential binding? Or, any intermediate data from Tobias pipeline that could be used for such analysis?

[msbentsen]

Hi,

Can you provide a little more information what is meant by "genotype-treatment interaction type analysis"? I am not familiar with the setup of the analysis.

If you have different conditions, e.g. control, treatment1, treatment2 etc., you can compare these pairwise using TOBIAS BINDetect - but that would generally be in the same genotype.

[ikumar2000]

Hi there...

An interaction type analysis is commonly performed during differential gene expression studies. For an example- the effect of treatment in one genotype was significantly different to the effect of treatment in another genotype. This would be referred to as "genotype-treatment interaction". One example in differential binding context would be- if a motif was found bound 2 fold more in genotype A (under treatment compared to control) however 4 fold more (or may be 2 fold less) in genotype B then most likely there is a genotype-treatment interaction. It needs to be statistically significant. 

[msbentsen]

Hi, thank you for the clarification. I believe this is the same as discussed https://github.com/loosolab/TOBIAS/issues/105. Unfortunately, such an advanced setup is not supported by TOBIAS.

However, you might get to the same information by comparing the pairwise differential TFs between (ctrl-genotypeA vs. treat-genotypeA), (ctrl-genotypeB vs. treat-genotypeB) and (treat-genotypeA vs. treat-genotypeB). This will be manual work though, and I am not sure if it will be possible to get a significance - but it might help to uncover influences of genotype and treatment individually.