i have a more general question (anchored in genomics and related to ChIP-seq) regarding the statistical tests to show the specificity of phenomenon :
let's consider an example: someone did a ChIP_seq for H3K27me3, and wants to show that H3K27me3 mark increases only on the genes involved in autophagy, after cell treatment ...
what type of analysis would you recommend in order to show that the phenomenon (ie increase in H3K27me3) is specific to a set of genes (ie autophagy genes) :
A -- taking random sets of non-autophagy genes (practically, the rest of the genes in the genome) -- and using parametric and non-parametric tests when comparing SET 1 (autophagy genes) with SET 2 (non-autophagy genes)
B -- using hypergeometric / fisher-tests on a matrix (autophagy/no-autophagy genes vs increase/no-increase in H3K27me3) ?
thanks a lot, and happy weekend ;) !