Table 3.

Statistics of metabolism pathway assignments and phylogenetic profile identities of gene families and singletons.

Pathway map number and name	Class	NGF/S	Fpw	Fall	E = Fpw/Fall	Adjusted p-value
00450 Selenocompound metabolism	MOAA	15	0.152	0.037	4.165	<0.001
00020 Citrate cycle (TCA cycle)	CM	31	0.146	0.035	4.145	<0.001
00920 Sulfur metabolism	EM	23	0.142	0.035	4.014	<0.001
00660 C5-Branched dibasic acid metabolism	CM	15	0.152	0.039	3.958	<0.001
00280 Valine. leucine and isoleucine degradation	AAM	26	0.120	0.036	3.377	<0.001
00710 Carbon fixation in photosynthetic organisms	EM	70	0.065	0.026	2.498	<0.001
00250 Alanine. aspartate and glutamate metabolism	AAM	43	0.063	0.026	2.467	<0.001
00400 Phenylalanine. tyrosine and tryptophan biosynthesis	AAM	49	0.061	0.028	2.188	<0.001
00010 Glycolysis/Gluconeogenesis	CM	105	0.050	0.024	2.134	<0.001
00260 Glycine. serine and threonine metabolism	AAM	75	0.049	0.024	2.068	<0.001
00620 Pyruvate metabolism	CM	72	0.047	0.024	2.000	<0.001
00240 Pyrimidine metabolism	NM	325	0.023	0.014	1.670	<0.001
00300 Lysine biosynthesis	AAM	16	0.125	0.034	3.682	0.006
00650 Butanoate metabolism	CM	25	0.097	0.035	2.746	0.006
00640 Propanoate metabolism	CM	41	0.070	0.029	2.428	0.006
00270 Cysteine and methionine metabolism	AAM	70	0.053	0.025	2.180	0.006
00480 Glutathione metabolism	MOAA	42	0.050	0.023	2.152	0.010
00030 Pentose phosphate pathway	CM	63	0.040	0.024	1.684	0.010
00071 Fatty acid degradation	LM	15	0.114	0.034	3.365	0.015
00945 Stilbenoid. diarylheptanoid and gingerol biosynthesis	BSM	12	0.152	0.012	12.553	0.024
00220 Arginine biosynthesis	AAM	41	0.041	0.022	1.865	0.030
00290 Valine. leucine and isoleucine biosynthesis	AAM	35	0.047	0.026	1.820	0.030
00630 Glyoxylate and dicarboxylate metabolism	CM	74	0.035	0.022	1.613	0.033
00051 Fructose and mannose metabolism	CM	65	0.034	0.021	1.616	0.035
00860 Porphyrin and chlorophyll metabolism	MCV	63	0.034	0.021	1.638	0.041
00410 beta-Alanine metabolism	MOAA	24	0.047	0.027	1.740	0.047
00230 Purine metabolism	NM	367	0.021	0.014	1.487	0.049
00310 Lysine degradation	AAM	13	0.077	0.037	2.060	0.050
00760 Nicotinate and nicotinamide metabolism	MCV	22	0.048	0.022	2.214	0.052
00904 Diterpenoid biosynthesis	MTP	7	0.143	0.012	11.626	0.069
00380 Tryptophan metabolism	AAM	35	0.039	0.022	1.730	0.091
00941 Flavonoid biosynthesis	BSM	14	0.066	0.014	4.695	0.097
00790 Folate biosynthesis	MCV	30	0.039	0.020	2.003	0.097

For all KEGG metabolism pathways given by their KEGG map number and name and with profiling results corresponding to a False Discovery Rate (FDR) of less than 10%, table lists the metabolism class to which pathway belongs indicated by their abbreviations introduced in Table 1, the number of gene families or singleton genes (referred to as gene objects, N_GF/S) annotated to them, the fraction of all profile-profile comparisons among all N_GF/S gene objects yielding identical profiles within a pathway (F_pw, Equation 1), the fraction of all profile-profile comparisons of N_GF/S gene objects yielding identical profiles within and to gene objects outside a pathway (F_all, Equation 2), the resulting fold enrichment (E = F_pw/F_all) of identical phylogenetic profiles within a pathway relative to expectation, and associated Benjamini-Hochberg corrected empirical p-value based on 10,000 random pathway assignments. Results are based on Network30-based gene family assignments (see Methods). Only pathways with significant enrichment of identical profiles (adjusted p-value < 0.1) are listed. For a complete listing of statistical results for all 94 pathways considered in this study, see Supplementary Table 1. Pathways belonging to secondary metabolism classes Biosynthesis of other secondary metabolites (BSM) and Metabolism of terpenoids and polyketides (MTP) are highlighted using bold face font. Pathways are sorted in ascending order of p-value.