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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M1">View MathML</a> 1.4 × 10−20
Enriched Individual Amino Acids Biosynthesis 99 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M2">View MathML</a> 4.0 × 10−19
Enriched Amino Acids Degradation 118 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M3">View MathML</a> 2.0 × 10−17
Enriched Purine Nucleotide Biosynthesis 19 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M4">View MathML</a> 3.2 × 10−10
Enriched Generation Of Precursor Metabolites And Energy 162 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M5">View MathML</a> 2.6 × 10−9
Enriched C1 Compounds Utilization And Assimilation 28 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M6">View MathML</a> 9.3 × 10−9
Enriched Autotrophic CO2 Fixation 7 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M7">View MathML</a> 1.3 × 10−7
Enriched CO2 Fixation 9 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M8">View MathML</a> 2.8 × 10−7
Enriched Vitamins Biosynthesis 68 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M9','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M9">View MathML</a> 1.4 × 10−6
Enriched Sugar Derivatives Degradation 42 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M10','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M10">View MathML</a> 3.8 × 10−6
Enriched Sugar Alcohols Degradation 12 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M11','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M11">View MathML</a> 6.0 × 10−6
Enriched Amines And Polyamines Biosynthesis 37 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M12">View MathML</a> 6.9 × 10−6
Enriched Carboxylates Degradation 44 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M13">View MathML</a> 1.0 × 10−5
Enriched Sugars Degradation 51 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M14','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M14">View MathML</a> 1.5 × 10−5
Enriched NAD Biosynthesis 8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M15">View MathML</a> 1.6 × 10−5
Enriched Fermentation 46 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M16','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M16">View MathML</a> 3.6 × 10−5
Enriched Nucleosides And Nucleotides Biosynthesis 35 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M17">View MathML</a> 6.8 × 10−5
Enriched Nucleosides And Nucleotides Degradation 29 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M18','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M18">View MathML</a> 1.4 × 10−4
Enriched Purine Nucleotide Salvage 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M19','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M19">View MathML</a> 1.7 × 10−4
Enriched Arginine Degradation 15 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M20">View MathML</a> 4.6 × 10−4
Enriched Purine Nucleotide De Novo Biosynthesis 6 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M21">View MathML</a> 4.9 × 10−4
Enriched Mandelates Degradation 2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M22','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M22">View MathML</a> 9.9 × 10−4
Enriched Gluconeogenesis 2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M23','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M23">View MathML</a> 1.1 × 10−3
Enriched Glycolysis 6 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M24','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M24">View MathML</a> 2.0 × 10−3
Enriched NAD Metabolism 11 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M25','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M25">View MathML</a> 2.1 × 10−3
Enriched Geranylgeranyldiphosphate Biosynthesis 3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M26','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M26">View MathML</a> 2.3 × 10−3
Enriched Catechol Degradation 7 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M27','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M27">View MathML</a> 2.3 × 10−3
Enriched Methionine Biosynthesis 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M28','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M28">View MathML</a> 4.0 × 10−3
Enriched Photosynthesis 5 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M29','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M29">View MathML</a> 4.0 × 10−3
Enriched Pyrimidine Nucleotide Biosynthesis 8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M30','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M30">View MathML</a> 5.7 × 10−3
Enriched Toluenes Degradation 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M31','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M31">View MathML</a> 7.2 × 10−3
Enriched Glutamate Degradation 10 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M32','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M32">View MathML</a> 1.5 × 10−2
Enriched Formaldehyde Assimilation 3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M33','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M33">View MathML</a> 1.6 × 10−2
Enriched Alcohols Degradation 17 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M34','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M34">View MathML</a> 1.6 × 10−2
Enriched Urate Degradation 2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M35','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M35">View MathML</a> 2.4 × 10−2
Enriched Cobalamin Biosynthesis 9 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M36','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M36">View MathML</a> 2.5 × 10−2
Depleted Secondary Metabolites Biosynthesis 460 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M37">View MathML</a> 3.8 × 10−35
Depleted Glucosinolates Biosynthesis 9 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M38','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M38">View MathML</a> 2.0 × 10−17
Depleted Biosynthesis 1182 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M39','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M39">View MathML</a> 2.3 × 10−16
Depleted Nitrogen Containing Glucosides Biosynthesis 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M40','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M40">View MathML</a> 8.0 × 10−15
Depleted Hormones Degradation 24 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M41','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M41">View MathML</a> 2.7 × 10−13
Depleted Polymeric Compounds Degradation 35 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M42','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M42">View MathML</a> 3.5 × 10−12
Depleted Polysaccharides Degradation 33 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M43','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M43">View MathML</a> 2.0 × 10−10
Depleted Steroids Degradation 8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M44','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M44">View MathML</a> 4.2 × 10−6
Depleted Polyketides Biosynthesis 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M45','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M45">View MathML</a> 1.5 × 10−5
Depleted Glucosinolates Degradation 4 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M46','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M46">View MathML</a> 7.0 × 10−5
Depleted Cholesterol Degradation 4 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M47','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M47">View MathML</a> 3.3 × 10−4
Depleted Fatty Acid Biosynthesis 49 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M48','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M48">View MathML</a> 3.4 × 10−4
Depleted Nitrogen Containing Secondary Compounds Degradation 18 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M49','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M49">View MathML</a> 1.0 × 10−3
Depleted Terpenoids Biosynthesis 127 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M50','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M50">View MathML</a> 1.2 × 10−3
Depleted Plant Hormones Degradation 15 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M51','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M51">View MathML</a> 1.6 × 10−3
Depleted Sesquiterpenoids Biosynthesis 32 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M52','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M52">View MathML</a> 1.6 × 10−3
Depleted Chlorotoluene Degradation 5 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M53','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M53">View MathML</a> 2.3 × 10−3
Depleted Auxins Degradation 8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M54','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M54">View MathML</a> 4.1 × 10−3
Depleted Apocarotenoids Biosynthesis 4 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M55','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M55">View MathML</a> 2.4 × 10−2
Depleted Lignans Biosynthesis 5 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M56','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M56">View MathML</a> 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.

Altman et al.

Altman et al. BMC Bioinformatics 2013 14:112   doi:10.1186/1471-2105-14-112

Open Data