Table 12

KEGG pathway classes that are significantly enriched or depleted for reactions with links to MetaCyc
Status Pathway class Class size Links p-value
Enriched Nucleotide And Amino Acid Metabolism 72 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M57','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M57">View MathML</a> 2.6 × 10−56
Enriched Carbohydrate Metabolism 15 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M58','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M58">View MathML</a> 4.1 × 10−29
Enriched Amino Acid Metabolism 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M59','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M59">View MathML</a> 3.0 × 10−20
Enriched Energy Metabolism 8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M60','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M60">View MathML</a> 2.9 × 10−14
Enriched Cofactor And Vitamin Biosynthesis 19 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M61','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M61">View MathML</a> 1.8 × 10−11
Enriched Energy Metabolism 24 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M62','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M62">View MathML</a> 1.3 × 10−10
Enriched Carbon Fixation 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M63','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M63">View MathML</a> 7.6 × 10−8
Enriched Aromatic Amino Acid Metabolism 11 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M64','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M64">View MathML</a> 2.2 × 10−5
Enriched Alkaloid And Other Secondary Metabolite Biosynthesis 4 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M65','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M65">View MathML</a> 2.9 × 10−5
Enriched Other Carbohydrate Metabolism 6 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M66','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M66">View MathML</a> 2.9 × 10−5
Enriched Nucleotide Metabolism 2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M67','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M67">View MathML</a> 7.6 × 10−5
Enriched Cysteine And Methionine Metabolism 6 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M68','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M68">View MathML</a> 3.4 × 10−4
Enriched Central Carbohydrate Metabolism 13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M69','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M69">View MathML</a> 4.4 × 10−4
Enriched Reaction Motif 3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M70','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M70">View MathML</a> 7.1 × 10−3
Enriched Arginine And Proline Metabolism 3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M71','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M71">View MathML</a> 7.1 × 10−3
Enriched Histidine Metabolism 2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M72','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M72">View MathML</a> 1.6 × 10−2
Enriched Purine Metabolism 3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M73','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M73">View MathML</a> 2.1 × 10−2
Depleted Xenobiotics Biodegradation And Metabolism 20 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M74','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M74">View MathML</a> 1.0 × 10−37
Depleted Glycan Biosynthesis And Metabolism 15 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M75','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M75">View MathML</a> 1.9 × 10−21
Depleted Metabolism Of Terpenoids And Polyketides 20 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M76','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M76">View MathML</a> 4.4 × 10−13
Depleted Glycan Metabolism 10 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M77','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M77">View MathML</a> 6.8 × 10−11
Depleted Glycosaminoglycan Metabolism 7 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M78','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M78">View MathML</a> 2.0 × 10−5
Depleted Lipid Metabolism 17 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/112/mathml/M79','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/112/mathml/M79">View MathML</a> 1.4 × 10−3

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 MetaCyc 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