sysbiochalmers / cellfactory-ecyeastgem Goto Github PK

• models construction
• share models

• Group of products based on tSNE using the predicted genes strategies.

• compare the gene targets from a general minimal condition and the in vivo experimental condition. -> generate venn diagrams comparing predictions with and without background

• compare the general trends using the output from step2 and step3

Also compare the predictions of previous methods and ecFSEOF with the experimental gene targets for these products:

• succinate

• 3HP

• FFAs

• Amorphadiene

• Also compare yields with GEMs, by adding experimental points to the corresponding yield plots

• various chemicals
• additional protein models

• Add reference (human metabolism)
• Add more references
• Check for other top-controlling genes

• 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