Pathway enrichment analysis

SysBioChalmers / CellFactory-ecYeastGEM

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

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Pathway enrichment analysis #18

Open IVANDOMENZAIN opened 3 years ago

IVANDOMENZAIN commented 3 years ago

[ ] 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
[x] 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 commented 3 years ago

@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 commented 3 years ago

You can check my upload scripts.

hongzhonglu commented 3 years ago

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