Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

Table 6 Relevant pathways for the phenotype 'periodontal disease causing'

Relevant pathway	Dataset	Attribute selection method
Biosynthesis of coenzyme B12 (coba1) ↑	4A, 4O, 3A, 3O	R, S, W
Biosynthesis of L-proline (proline1) ↓	4A, 4O, 3A, 3O	R, S, W
Glutamate fermentation (fnc1) ↑	4A, 4O, 3A, 3O	R, S, W
Biosynthesis of 5-formimino-THF (c2) ↑	4A, 4O, 3A, 3O	R, S
Urea cycle (part) (urea2) ↓	4A, 4O, 3A, 3O	R, S
Conversion of L-glutamate to L-proline (glutamate3) ↓	4A, 4O, 3A, 3O	R, S
Conversion of L-glutamate to L-ornithine (glutamate2) ↓	4A, 4O, 3A, 3O	R
Degradation of L-histidine to L-glutamate (histidine2) ↑	4O, 3A, 3O	R, S, W
Glycolysis and Gluconeogenesis (part) (gg13) ↑	4A, 4O, 3O	R, S

The pathways that are among the ten most relevant pathways for at least one attribute selection method (R, ReliefF; S, SVMAttributeEval; W, wrapper(naïve Bayes)) and for at least three of the four investigated datasets (4A, 'periodontal disease causing' genomes in complete dataset (266 genomes); 4O, 'periodontal disease causing' genomes in oral cavity dataset (15 genomes); 3A, 'members of red or orange cluster' in the complete dataset; 3O, 'members of red or orange cluster' in oral cavity dataset) are listed. An upwards pointing arrow denotes pathways that are relevant due to higher pathway scores (that is, pathways are more complete) for the periodontal species compared to the other genomes in the investigated dataset. In analogy, a downwards pointing arrow denotes pathways that are relevant due to lower pathway scores (that is, pathways are less complete) for the periodontal species.

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