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mgtools / MinPath

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
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pathway completeness #3

Open jsgounot opened 3 years ago

jsgounot commented 3 years ago

hi,

thanks for your tool ! I'm new to the pathway analysis and have quite a basic question: I imagine that pathway reported by MinPath are not all complete. I guess that's what is actually reported in the output with fam0 and fam-found: Total number of reaction and number of reactions found in the dataset. Am I right ?

Thanks ! jsgounot

KristinaGagalova commented 6 months ago

This is in the readme of MinPath - I believe fam-found are the annotated reactions in the dataset indeed

 ...
    path 00030 kegg n/a  naive 1  minpath 1  fam0  42  fam-found  18  name  Pentose phosphate pathway
    path 00031 kegg n/a  naive 1  minpath 0  fam0  12  fam-found  2  name  Inositol metabolism
    ...
    1) path 00030, path 00031 are the KEGG pathway IDs (if your input file has fig families, the pathways will then be SEED subsystems)
    2) kegg n/a, indicates pathway reconstruction of your input dataset if not available (note: this information is only available for the genomes annotated
         in KEGG database); for input with fig families, KEGG is replaced by SEED
    3) naive 1 or 0: the pathway is reconstructed, or not, by the naive mapping approach
    4) minpath 1 or 0: the pathway is kept, or removed by MinPath
    5) fam0: the total number of families involved in the corresponding pathway
    6) fam-found: the total number of involved families that are annotated
    7) name: the description of the corresponding pathway (subsystem)