Pathway enrichment analysis

[IVANDOMENZAIN]

• Perform analysis for each chemical on the final list of targets (compatible_genes_results).

• Check if there is overlap of enriched pathways across chemicals for each family

• Run enrichment analysis for overlaped OE targets within a family (present in at least 50% of the chemicals in the family)

• Repeat the last point but for KD + KO

[hongzhonglu]

@IVANDOMENZAIN Hi Iven, so here we choose common genes targets for all products from one families and then do the enrichment analysis? I found for protein families, no common genes targets for the knock out, only a few genes targets for the knock down and 6 gene targets for OE.. Then we can't do enrichment analysis for these three strategies as the gene number is very limited.

[hongzhonglu]

You can check my upload scripts.

[hongzhonglu]

Will do it as discussed:

1. enrichment analysis for each product and find the common enriched pathways across one family
2. enrichment analysis of top genes from part of products from one family