Table 1.
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Example GO terms significantly enriched with phenotype-associated gene families
PhenotypeGO termFDR originalFDR inferredOR originalOR inferred
gelatin hydrolysispeptidase activityn.s.5%n.s.86.4
iron-reduceriron ion binding22%1%12.511.2
halophilicsodium ion transportn.s.7×10-5n.s.38.9
energy source = photosyntheticpigment biosynthesis20%1%5.09.3
pathogenic in mammalspathogenesis29%3%4.78.6
lactic/cheese/food/ferment/milkgalactose metabolic processNA1%NA52.6
legum/symbiosis/rhizobia/nod/stemnitrogen fixationNA3×10-6NA1362.6
PhenotypeGO termFDR originalFDR inferredOR originalOR inferred
gelatin hydrolysispeptidase activityn.s.5%n.s.86.4
iron-reduceriron ion binding22%1%12.511.2
halophilicsodium ion transportn.s.7×10-5n.s.38.9
energy source = photosyntheticpigment biosynthesis20%1%5.09.3
pathogenic in mammalspathogenesis29%3%4.78.6
lactic/cheese/food/ferment/milkgalactose metabolic processNA1%NA52.6
legum/symbiosis/rhizobia/nod/stemnitrogen fixationNA3×10-6NA1362.6

Association of genes to phenotypes is determined by a t-test on the logistic regression coefficient, requiring FDR < 10%. Table shows the examples in which the GO-phenotype association was not significant in the sets of gene families retrieved using the original set of phenotypic labels, but became significant as the inferred phenotypic labels were also considered. The FDR column is by Fisher's exact test for COG-GO association by Fisher's exact test, one-tailed. ‘OR’, odds ratio. ‘n.s.’ denotes associations that did not have statistically significant gene-trait associations; Supplementary Methods). ‘NA’ denotes that NMF phenotypic concepts were not available in the original data.

Table 1.
Open in new tab
Example GO terms significantly enriched with phenotype-associated gene families
PhenotypeGO termFDR originalFDR inferredOR originalOR inferred
gelatin hydrolysispeptidase activityn.s.5%n.s.86.4
iron-reduceriron ion binding22%1%12.511.2
halophilicsodium ion transportn.s.7×10-5n.s.38.9
energy source = photosyntheticpigment biosynthesis20%1%5.09.3
pathogenic in mammalspathogenesis29%3%4.78.6
lactic/cheese/food/ferment/milkgalactose metabolic processNA1%NA52.6
legum/symbiosis/rhizobia/nod/stemnitrogen fixationNA3×10-6NA1362.6
PhenotypeGO termFDR originalFDR inferredOR originalOR inferred
gelatin hydrolysispeptidase activityn.s.5%n.s.86.4
iron-reduceriron ion binding22%1%12.511.2
halophilicsodium ion transportn.s.7×10-5n.s.38.9
energy source = photosyntheticpigment biosynthesis20%1%5.09.3
pathogenic in mammalspathogenesis29%3%4.78.6
lactic/cheese/food/ferment/milkgalactose metabolic processNA1%NA52.6
legum/symbiosis/rhizobia/nod/stemnitrogen fixationNA3×10-6NA1362.6

Association of genes to phenotypes is determined by a t-test on the logistic regression coefficient, requiring FDR < 10%. Table shows the examples in which the GO-phenotype association was not significant in the sets of gene families retrieved using the original set of phenotypic labels, but became significant as the inferred phenotypic labels were also considered. The FDR column is by Fisher's exact test for COG-GO association by Fisher's exact test, one-tailed. ‘OR’, odds ratio. ‘n.s.’ denotes associations that did not have statistically significant gene-trait associations; Supplementary Methods). ‘NA’ denotes that NMF phenotypic concepts were not available in the original data.

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