Chip seq remove the genes which has very low enrichment

Question

[Lalita]

Hello I am doing a metagene analysis chipseq for three set of (data1(1000genes), data2(1500), data3(10000)) of gene list in which I wanted compare this three groups of genes TSS and genebody regions which group has the higher enrichment any one suggest me how can I do this and before comparison average accross genes in TSS or genebody I wanted remove the genes which are very low enrichment acrross TSS and genebody any tool or suggestions how can I proceed.

1. My gene list number is vary different is it good idea to compare this gene list like this or is there any method I can adopt

I am new to chip seq data analysis please help me

Thank you