What this entity is
Canonical name: Fisher’s exact test. 1
Type: Method. 1
Known aliases: Fisher’s exact tests. 1
Stable external identifier: None reported in the source. 1
Key facts from the documents
Fisher’s exact tests evaluate categorical enrichment and depletion. They were used for metal-resistance patterns in a 5° global grid containing 289 cells with at least 5 MAGs. With Benjamini–Hochberg false discovery rate (BH FDR) correction, the analysis identified 11 significant hotspots with OR>2 and q<0.05, plus 3 coldspots with OR<0.5 and q<0.05. 1
The top hotspot was the Atacama/Andean region of Chile at lat=-25°, lon=-70°, with 21.8% prevalence, OR=9.83, q=7.6e-12, and n=101 MAGs. Eastern and central USA clusters at lat=40°, lon=-80° and -90° had OR=7.9 and 6.3, respectively; an East/Southeast Asia cluster at lat=25–30°, lon=105–120° had OR=4.4–5.9. 1
Biome-stratified tests compared each biome with the global baseline and applied BH FDR correction. Soil showed 5.8% prevalence, OR=5.05, and q=1.8e-82 among 7,939 MAGs; rhizosphere showed 1.9% prevalence, OR=0.66, and q=0.30 (NS) among 422 MAGs; marine samples showed 1.2% prevalence, OR=0.20, and q=9.2e-80 among 13,995 MAGs. 1
The PGP pangenome analysis used the same exact-test framework for categorical gene co-occurrence and environmental comparisons: eight of 10 focal-gene pairs remained significant after BH-FDR correction, including positive pqqC × acdS association (OR = 7.24, n = 286, q = 1.2e-83) and negative nifH × hcnC association (OR = 0.23, q = 5.8e-29). 2 This supports using the method for discrete ecological enrichment and depletion beyond metal resistance. 2
The PGP analysis also found acdS enrichment in soil/rhizosphere species (OR = 7.02, q = 5.1e-62) and nifH depletion (OR = 0.60, q = 5.5e-08), while a Fisher test linked ipdC to complete tryptophan biosynthesis (OR = 2.81, p = 6.3e-10). 2 These findings refine the biome-level use case by showing that exact tests can compare gene-pair associations and environment-stratified species prevalences, although the soil-specific ipdC reversal is hypothesis-generating. 2
The conservation-versus-fitness analysis applied Fisher’s exact test to essential-gene status versus pangenome conservation, finding that essential genes were 86.1% core versus 81.2% for non-essential genes, with a median odds ratio of 1.56; 18 of 33 organisms showed significant enrichment after BH-FDR correction at q < 0.05. 3 This supports the method’s use for testing modest categorical conservation effects, while the study’s single-condition RB-TnSeq essentiality calls and variable pangenome coverage refine interpretation of the resulting associations. 3
The prophage–AMR analysis applied Fisher’s exact test to compare accessory status: AMR genes within 10 genes of a prophage marker were 67.6% accessory, versus 65.5% for distal AMR genes, with OR=1.10, one-sided p=0.005, and bootstrap 95% confidence interval [1.024, 1.185]. 4 This supports the method’s sensitivity to modest categorical effects, while the 2.1 percentage point difference and threshold-dependent odds ratios (0.78 at 3 genes, 0.92 at 5, 1.10 at 10, 1.19 at 15, and 1.28 at 50) refine interpretation: statistical significance need not imply a large or consistently replicated effect. 4
These results contribute to environmental-resistome, which synthesizes geographic and biome-level patterns in environmental metal resistance. They also relate to environment-embedding-geography, because sampling-effort correction is necessary before regional hotspot patterns can be interpreted. The conservation result contributes to gene-essentiality and pangenome-integration by testing essentiality against core-genome membership. The method is related to benjamini-hochberg-fdr, the multiple-testing correction used with the reported tests.
Complete source contexts are summarized in Global Biogeography of Environmental Bacterial Metal Resistance, PGP Gene Distribution Across Environments & Pangenomes, Prophage-AMR Co-mobilization Atlas, and Conservation vs Fitness — Linking FB Genes to Pangenome Clusters.