Table 11.

MetaCyc pathway classes that are significantly enriched or depleted for reactions with links to KEGG

Status	Pathway class	Class size	Links	p-value
Enriched	Amino Acids Biosynthesis	112	$\frac{186}{260}$	1.4 × 10−20
Enriched	Individual Amino Acids Biosynthesis	99	$\frac{174}{244}$	4.0 × 10−19
Enriched	Amino Acids Degradation	118	$\frac{222}{326}$	2.0 × 10−17
Enriched	Purine Nucleotide Biosynthesis	19	$\frac{46}{56}$	3.2 × 10−10
Enriched	Generation Of Precursor Metabolites And Energy	162	$\frac{170}{304}$	2.6 × 10−9
Enriched	C1 Compounds Utilization And Assimilation	28	$\frac{75}{102}$	9.3 × 10−9
Enriched	Autotrophic CO2 Fixation	7	$\frac{47}{57}$	1.3 × 10−7
Enriched	CO2 Fixation	9	$\frac{48}{59}$	2.8 × 10−7
Enriched	Vitamins Biosynthesis	68	$\frac{128}{223}$	1.4 × 10−6
Enriched	Sugar Derivatives Degradation	42	$\frac{109}{162}$	3.8 × 10−6
Enriched	Sugar Alcohols Degradation	12	$\frac{54}{68}$	6.0 × 10−6
Enriched	Amines And Polyamines Biosynthesis	37	$\frac{57}{74}$	6.9 × 10−6
Enriched	Carboxylates Degradation	44	$\frac{82}{132}$	1.0 × 10−5
Enriched	Sugars Degradation	51	$\frac{108}{162}$	1.5 × 10−5
Enriched	NAD Biosynthesis	8	$\frac{23}{23}$	1.6 × 10−5
Enriched	Fermentation	46	$\frac{75}{106}$	3.6 × 10−5
Enriched	Nucleosides And Nucleotides Biosynthesis	35	$\frac{69}{128}$	6.8 × 10−5
Enriched	Nucleosides And Nucleotides Degradation	29	$\frac{64}{90}$	1.4 × 10−4
Enriched	Purine Nucleotide Salvage	13	$\frac{26}{28}$	1.7 × 10−4
Enriched	Arginine Degradation	15	$\frac{35}{42}$	4.6 × 10−4
Enriched	Purine Nucleotide De Novo Biosynthesis	6	$\frac{22}{30}$	4.9 × 10−4
Enriched	Mandelates Degradation	2	$\frac{18}{18}$	9.9 × 10−4
Enriched	Gluconeogenesis	2	$\frac{23}{28}$	1.1 × 10−3
Enriched	Glycolysis	6	$\frac{27}{30}$	2.0 × 10−3
Enriched	NAD Metabolism	11	$\frac{28}{33}$	2.1 × 10−3
Enriched	Geranylgeranyldiphosphate Biosynthesis	3	$\frac{18}{18}$	2.3 × 10−3
Enriched	Catechol Degradation	7	$\frac{17}{17}$	2.3 × 10−3
Enriched	Methionine Biosynthesis	13	$\frac{29}{34}$	4.0 × 10−3
Enriched	Photosynthesis	5	$\frac{24}{30}$	4.0 × 10−3
Enriched	Pyrimidine Nucleotide Biosynthesis	8	$\frac{36}{53}$	5.7 × 10−3
Enriched	Toluenes Degradation	13	$\frac{35}{46}$	7.2 × 10−3
Enriched	Glutamate Degradation	10	$\frac{28}{35}$	1.5 × 10−2
Enriched	Formaldehyde Assimilation	3	$\frac{24}{28}$	1.6 × 10−2
Enriched	Alcohols Degradation	17	$\frac{24}{30}$	1.6 × 10−2
Enriched	Urate Degradation	2	$\frac{17}{18}$	2.4 × 10−2
Enriched	Cobalamin Biosynthesis	9	$\frac{35}{46}$	2.5 × 10−2
Depleted	Secondary Metabolites Biosynthesis	460	$\frac{579}{1896}$	3.8 × 10−35
Depleted	Glucosinolates Biosynthesis	9	$\frac{4}{104}$	2.0 × 10−17
Depleted	Biosynthesis	1182	$\frac{1459}{4215}$	2.3 × 10−16
Depleted	Nitrogen Containing Glucosides Biosynthesis	13	$\frac{11}{125}$	8.0 × 10−15
Depleted	Hormones Degradation	24	$\frac{12}{124}$	2.7 × 10−13
Depleted	Polymeric Compounds Degradation	35	$\frac{17}{136}$	3.5 × 10−12
Depleted	Polysaccharides Degradation	33	$\frac{17}{127}$	2.0 × 10−10
Depleted	Steroids Degradation	8	$\frac{2}{46}$	4.2 × 10−6
Depleted	Polyketides Biosynthesis	13	$\frac{6}{62}$	1.5 × 10−5
Depleted	Glucosinolates Degradation	4	$\frac{0}{30}$	7.0 × 10−5
Depleted	Cholesterol Degradation	4	$\frac{1}{33}$	3.3 × 10−4
Depleted	Fatty Acid Biosynthesis	49	$\frac{20}{354}$	3.4 × 10−4
Depleted	Nitrogen Containing Secondary Compounds Degradation	18	$\frac{13}{77}$	1.0 × 10−3
Depleted	Terpenoids Biosynthesis	127	$\frac{176}{530}$	1.2 × 10−3
Depleted	Plant Hormones Degradation	15	$\frac{7}{55}$	1.6 × 10−3
Depleted	Sesquiterpenoids Biosynthesis	32	$\frac{25}{114}$	1.6 × 10−3
Depleted	Chlorotoluene Degradation	5	$\frac{0}{24}$	2.3 × 10−3
Depleted	Auxins Degradation	8	$\frac{0}{23}$	4.1 × 10−3
Depleted	Apocarotenoids Biosynthesis	4	$\frac{0}{20}$	2.4 × 10−2
Depleted	Lignans Biosynthesis	5	$\frac{0}{20}$	2.4 × 10−2

Class size is the number of pathway instances for the given pathway class. The ‘Links’ column is the number of reactions among the pathways of the pathway class that have links to KEGG reactions, over the total number of reactions for the pathway class. The Bonferroni-corrected p-value from the hypergeometric test indicates the probability that the observed proportion of reactions with links within the pathway occurred by chance. Pathways with a p-value at or below a cut-off of α = 0.025 are shown. The full list may be found in the Additional file 2.