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Table 1 FMAP performs pathway analysis of a Crohn’s disease study

From: FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Pathway KO Count Pathway Coverage P-value
Flagellar assembly 23 0.622 2.977 × 10−25
Bacterial chemotaxis 13 0.500 4.331 × 10−13
Synthesis and degradation of ketone bodies 2 0.250 2.798 × 10−2
Pentose and glucuronate interconversions 8 0.131 9.820 × 10−4
Glutathione metabolism 5 0.125 1.077 × 10−2
Porphyrin and chlorophyll metabolism 10 0.094 3.110 × 10−3
Butanoate metabolism 7 0.085 2.087 × 10−2
Glycine, serine and threonine metabolism 7 0.075 3.810 × 10−2
Glyoxylate and dicarboxylate metabolism 7 0.074 4.201 × 10−2
Two-component system 23 0.054 1.933 × 10−2
  1. FMAP can automatically streamline its built-in pathway analysis. Here we show the FMAP pathway analysis results of a Crohn’s disease study (Sequence Read Archive number: SRP002423). KO Count: number of differentially abundant (DA) genes detected by FMAP; Pathway coverage: normalized coverage in each pathway; P-value: Fisher’s exact test used to assess the over/under representation of DA genes