Figure 6

KEGG pathway enrichment analysis. The number of gene pair relationships within the same pathway plotted against an increasing graph size, given in gene number. The RA method, red, MI, blue, PE, green. Only pathways with gene % ≥25 for at least one method at graph size ~3000 genes are included in the figure. Pathways detected early in the graphs are: ribosome, proteasome, spliceosome, RNA transport. Pathways picked up by the RA method more strongly than PE and MI are both basic cell function pathways as well as disease related ones, such as: spliceosome, RNA transport, mRNA surveillance, and citrate cycle TCA cycle. Slightly stronger: proteasome, ubiquitin mediated proteolysis, Parkinson’s disease, oxidative phosphorylation, and Huntington’s disease. Pathways picked up equally well by all three methods are ribosome, ribosome biogenesis in eukaryotes, and Alzheimer’s disease. Where PE and MI methods do better than the RA model is in pathways protein processing in ER, mismatch repair, and DNA replication. Dashed lines represent the perturbed runs simulating the actual pathway.