Pathway-pathway level association

[jcasadogp]

Hi!

I have been working with Reactome in R for single cell RNA seq analysis. I wanted to get, not only the pathways corresponding to my genes, but also the pathway level they belong to so I could classify my results by pathway categories.

I had found these files in the Download section of Reactome:

There, they only expand the information part for the two first files, but not for the third (Complexes to Pathways (Human)), which is actually the one where I think the pathway-level association comes:

complex	pathway	top_level_pathway
R-ALL-1006146	R-HSA-977606	R-HSA-168256
R-ALL-113656	R-HSA-113501	R-HSA-1640170
R-ALL-2239507	R-HSA-3000480	R-HSA-5653656
R-ALL-2239507	R-HSA-3000497	R-HSA-5653656

I manually made and R vector that associates the top_level_pathway code with its name:

levelname_assignments <- c(
  "R-HSA-168256"  = "Immune System",
  "R-HSA-1640170" = "Cell Cycle",
  "R-HSA-5653656" = "Vesicle-mediated transport",
  "R-HSA-1430728" = "Metabolism",
  "R-HSA-1643685" = "Disease",
  "R-HSA-392499"  = "Metabolism of proteins",
  "R-HSA-1266738" = "Developmental Biology",
  "R-HSA-8953854" = "Metabolism of RNA",
  "R-HSA-9748784" = "Drug ADME",
  "R-HSA-74160"   = "Gene expression (Transcription)",
  "R-HSA-8953897" = "Cellular responses to stimuli",
  "R-HSA-162582"  = "Signal Transduction",
  "R-HSA-1500931" = "Cell-Cell communication",
  "R-HSA-5357801" = "Programmed Cell Death",
  "R-HSA-109582"  = "Hemostasis",
  "R-HSA-112316"  = "Neuronal System",
  "R-HSA-73894"   = "DNA Repair",
  "R-HSA-1852241" = "Organelle biogenesis and maintenance",
  "R-HSA-382551"  = "Transport of small molecules",
  "R-HSA-9709957" = "Sensory Perception",
  "R-HSA-1474244" = "Extracellular matrix organization",
  "R-HSA-397014"  = "Muscle contraction",
  "R-HSA-4839726" = "Chromatin organization",
  "R-HSA-1474165" = "Reproduction",
  "R-HSA-9612973" = "Autophagy",
  "R-HSA-9609507" = "Protein localization",
  "R-HSA-400253"  = "Circadian Clock",
  "R-HSA-69306"   = "DNA Replication",
  "R-HSA-8963743" = "Digestion and absorption"
)

However, I found that this third file (Complexes to Pathways (Human)) does not contain ALL the pathways (at least, not the Homo Sapiens one). Do you know where I can obtain it? Do you know any other way of obtaining these pathways' level?

I have developed some R code that uses all this information to match the pathway analysis with the pathway level, but I somehow feel it is not complete! I'd be very happy to discuss it!

Thank you in advance!