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Table 3 Pathways absent in lineages under positive selection

From: Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates

Under-Represented KEGG pathways TAED
KEGG Pathway Mapped Lineages Under Positive Selection Lineages Under Positive Selection Mapped Uncorrected P-value FDR P-value Bonferroni P-value
Zeatin biosynthesis 0.53% <  0.01% 0.0001 0.0006 0.0562
D-Arginine and D-ornithine metabolism 1.12% <  0.01% 0.0016 0.0056 0.5896
Penicillin and cephalosporin biosynthesis 1.12% <  0.01% 0.0016 0.0056 0.5896
Indole alkaloid biosynthesis 0.89% <  0.01% <  0.0001 <  0.0001 0.0011
Bacterial secretion system 1.40% <  0.01% 0.0013 0.0047 0.4768
Toluene degradation 2.53% 0.01% 0.0138 0.0422 1.0000
Fluorobenzoate degradation 2.53% 0.01% 0.0138 0.0422 1.0000
Chlorocyclohexane and chlorobenzene degradation 2.53% 0.01% 0.0138 0.0422 1.0000
Styrene degradation 1.37% 0.01% <  0.0001 <  0.0001 <  0.0001
Tropane_ piperidine and pyridine alkaloid biosynthesis 3.25% 0.02% 0.0014 0.0052 0.5283
Cyanoamino acid metabolism 4.07% 0.06% 0.0023 0.0080 0.8550
Maturity onset diabetes of the young 4.11% 0.08% 0.0004 0.0014 0.1353
Phototransduction - fly 1.64% 0.09% <  0.0001 <  0.0001 <  0.0001
MAPK signaling pathway - plant 4.42% 0.11% 0.0014 0.0052 0.5399
Glycosaminoglycan biosynthesis - keratan sulfate 3.51% 0.11% <  0.0001 <  0.0001 <  0.0001
Glycosaminoglycan biosynthesis - heparan sulfate / heparin 4.06% 0.11% <  0.0001 0.0001 0.0061
Thyroid cancer 2.78% 0.12% <  0.0001 <  0.0001 <  0.0001
Mannose type O-glycan biosynthesis 4.56% 0.15% 0.0010 0.0037 0.3723
RNA polymerase 2.96% 0.15% <  0.0001 <  0.0001 <  0.0001
Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 4.95% 0.16% 0.0171 0.0506 1.0000
Phototransduction 3.79% 0.17% <  0.0001 <  0.0001 <  0.0001
Nicotine addiction 4.07% 0.21% <  0.0001 <  0.0001 <  0.0001
Collecting duct acid secretion 5.06% 0.22% 0.0158 0.0472 1.0000
Pathogenic Escherichia coli infection 3.61% 0.23% <  0.0001 <  0.0001 <  0.0001
Hedgehog signaling pathway - fly 3.88% 0.23% <  0.0001 <  0.0001 <  0.0001
  1. The KEGG pathways with the lowest % of lineages under positive selection mapping to a pathway. All pathways were significant at the 0.05 level after correction with the false discovery rate (FDR). Bold numbers indicate not significant at the 0.05 level. Lineages with dN/dS > 1 considered under positive selection