Spreadsheet: f4a53cb3-aee9-45dc-92a6-58500e1a065f
Sheet: Table_S7

Table S7: PANTHER enrichment for genes 100kb up- and downstream of SNPs showing suggestive p-values in tests of association
A) High Pygmy LSBL SNPs
[NAME] | REFLIST (19911) | Genes Observed (1052) | Genes Expected | p-value
Muscarinic acetylcholine receptor 1 and 3 signaling pathway | 61 | 14 | 3.24 | 1e-05
Oxytocin receptor mediated signaling pathway | 60 | 13 | 3.19 | 3e-05
5HT2 type receptor mediated signaling pathway | 69 | 14 | 3.66 | 3e-05
Histamine H1 receptor mediated signaling pathway | 47 | 11 | 2.5 | 6e-05
Thyrotropin-releasing hormone receptor signaling pathway | 62 | 12 | 3.29 | 0.00016
Alpha adrenergic receptor signaling pathway | 32 | 8 | 1.7 | 0.00038
Metabotropic glutamate receptor group III pathway | 73 | 12 | 3.88 | 0.00068
Ionotropic glutamate receptor pathway | 54 | 10 | 2.87 | 0.00077
B cell activation | 82 | 12 | 4.35 | 0.00179
Wnt signaling pathway | 317 | 30 | 16.83 | 0.00217
[NAME] signaling pathway-Gq alpha and Go alpha mediated pathway | 134 | 16 | 7.11 | 0.00271
Metabotropic glutamate receptor group I pathway | 36 | 7 | 1.91 | 0.00352
Huntington disease | 167 | 17 | 8.87 | 0.00942
Endothelin signaling pathway | 91 | 11 | 4.83 | 0.0107
Alzheimer disease-amyloid secretase pathway | 71 | 9 | 3.77 | 0.0151
Blood coagulation | 48 | 7 | 2.55 | 0.0154
Inflammation mediated by chemokine and cytokine signaling pathway | 283 | 24 | 15.02 | 0.019
Muscarinic acetylcholine receptor 2 and 4 signaling pathway | 62 | 8 | 3.29 | 0.0193
p53 pathway | 113 | 12 | 6 | 0.0197
VEGF signaling pathway | 75 | 9 | 3.98 | 0.0206
Metabotropic glutamate receptor group II pathway | 51 | 7 | 2.71 | 0.0207
5HT4 type receptor mediated signaling pathway | 31 | 5 | 1.65 | 0.0262
Axon guidance mediated by semaphorins | 43 | 6 | 2.28 | 0.0289
Beta2 adrenergic receptor signaling pathway | 44 | 6 | 2.34 | 0.0318
[NAME] adrenergic receptor signaling pathway | 44 | 6 | 2.34 | 0.0318
5HT1 type receptor mediated signaling pathway | 44 | 6 | 2.34 | 0.0318
B) XP-EHH SNPs in Pygmies
[NAME] | REFLIST (19911) | Genes Observed (156) | Genes Expected | p-value
B cell activation | 82 | 5 | 0.64 | 0.000511
[NAME] biosynthesis | 1 | 1 | 0.01 | 0.0078
T cell activation | 102 | 4 | 0.8 | 0.00883
Integrin signaling pathway | 181 | 5 | 1.42 | 0.0145
5HT2 type receptor mediated signaling pathway | 69 | 3 | 0.54 | 0.0174
Alzheimer disease-amyloid secretase pathway | 71 | 3 | 0.56 | 0.0188
Metabotropic glutamate receptor group I pathway | 36 | 2 | 0.28 | 0.0329
C) iHS SNPs in Pygmies
[NAME] | REFLIST (19911) | Genes Observed (1121) | Genes Expected | p-value
5HT2 type receptor mediated signaling pathway | 69 | 10 | 3.88 | 0.00661
Oxytocin receptor mediated signaling pathway | 60 | 9 | 3.38 | 0.00787
VEGF signaling pathway | 75 | 10 | 4.22 | 0.0114
T cell activation | 102 | 12 | 5.74 | 0.0146
Integrin signaling pathway | 181 | 18 | 10.19 | 0.0164
EGF receptor signaling pathway | 135 | 14 | 7.6 | 0.0234
Thyrotropin-releasing hormone receptor signaling pathway | 62 | 8 | 3.49 | 0.0262
Angiogenesis | 191 | 17 | 10.75 | 0.0466
D) Enrichment for genes 100kb up- and downstream of SNPs showing raw p-values in the genome-wide EMMAX analysis less than 0.001 in the combined Pygmy-Bantu dataset
[NAME] | REFLIST (19911) | Genes Observed (1100) | Genes Expected | p-value
Insulin/IGF pathway-protein kinase B signaling cascade | 89 | 13 | 4.92 | 0.0017
Insulin/IGF pathway-mitogen activated protein kinase kinase/MAP kinase cascade | 35 | 6 | 1.93 | 0.0142
Alzheimer disease-amyloid secretase pathway | 71 | 9 | 3.92 | 0.0189
Methylmalonyl pathway | 4 | 2 | 0.22 | 0.0211
Adrenaline and noradrenaline biosynthesis | 32 | 5 | 1.77 | 0.034
Nicotinic acetylcholine receptor signaling pathway | 97 | 10 | 5.36 | 0.0464
E) Within 100kb of a SNP in Pygmy samples only with  p-value < 0.001 using EMMAX
[NAME] | REFLIST (19911) | Genes Observed (1041) | Genes Expected | p-value
Inflammation mediated by chemokine and cytokine signaling pathway | 283 | 33 | 14.8 | 2.65e-05
Glycolysis | 25 | 8 | 1.31 | 6.55e-05
Oxytocin receptor mediated signaling pathway | 60 | 11 | 3.14 | 0.000411
5HT2 type receptor mediated signaling pathway | 69 | 11 | 3.61 | 0.00126
Thyrotropin-releasing hormone receptor signaling pathway | 62 | 9 | 3.24 | 0.0061
Endothelin signaling pathway | 91 | 11 | 4.76 | 0.00964
Metabotropic glutamate receptor group I pathway | 36 | 6 | 1.88 | 0.0126
De novo pyrmidine ribonucleotides biosythesis | 18 | 4 | 0.94 | 0.0155
Ascorbate degradation | 4 | 2 | 0.21 | 0.019
Fructose galactose metabolism | 12 | 3 | 0.63 | 0.0259
Alpha adrenergic receptor signaling pathway | 32 | 5 | 1.67 | 0.0278
Cell cycle | 22 | 4 | 1.15 | 0.0295
Beta2 adrenergic receptor signaling pathway | 44 | 6 | 2.3 | 0.0298
[NAME] adrenergic receptor signaling pathway | 44 | 6 | 2.3 | 0.0298
Alzheimer disease-amyloid secretase pathway | 71 | 8 | 3.71 | 0.0355
Histamine H1 receptor mediated signaling pathway | 47 | 6 | 2.46 | 0.039
Xanthine and guanine salvage pathway | 6 | 2 | 0.31 | 0.04
Angiogenesis | 191 | 16 | 9.99 | 0.0474
F) Within 100kb of a SupportMix BIN with p-value < 0.05
[NAME] | REFLIST (19911) | Genes Observed (1525) | Genes Expected | p-value
Nicotinic acetylcholine receptor signaling pathway | 97 | 21 | 7.43 | 3.19e-05
Inflammation mediated by chemokine and cytokine signaling pathway | 283 | 40 | 21.68 | 0.00024
Oxytocin receptor mediated signaling pathway | 60 | 13 | 4.6 | 0.00095
Alpha adrenergic receptor signaling pathway | 32 | 9 | 2.45 | 0.000983
5HT2 type receptor mediated signaling pathway | 69 | 14 | 5.28 | 0.00114
Thyrotropin-releasing hormone receptor signaling pathway | 62 | 12 | 4.75 | 0.00361
Histamine H1 receptor mediated signaling pathway | 47 | 10 | 3.6 | 0.00397
Insulin/IGF pathway-protein kinase B signaling cascade | 89 | 15 | 6.82 | 0.00444
Cytoskeletal regulation by Rho GTPase | 98 | 16 | 7.51 | 0.00454
Metabotropic glutamate receptor group I pathway | 36 | 8 | 2.76 | 0.0074
TGF-beta signaling pathway | 145 | 20 | 11.11 | 0.00995
Alzheimer disease-amyloid secretase pathway | 71 | 12 | 5.44 | 0.01
Blood coagulation | 48 | 9 | 3.68 | 0.0131
Muscarinic acetylcholine receptor 1 and 3 signaling pathway | 61 | 10 | 4.67 | 0.0213
Beta2 adrenergic receptor signaling pathway | 44 | 8 | 3.37 | 0.0219
[NAME] adrenergic receptor signaling pathway | 44 | 8 | 3.37 | 0.0219
[NAME] signaling pathway-Gi alpha and [NAME] alpha mediated pathway | 166 | 20 | 12.71 | 0.0348
PI3 kinase pathway | 115 | 15 | 8.81 | 0.0351
Huntington disease | 167 | 20 | 12.79 | 0.0366
Ascorbate degradation | 4 | 2 | 0.31 | 0.0383
Adrenaline and noradrenaline biosynthesis | 32 | 6 | 2.45 | 0.0387
Histamine H2 receptor mediated signaling pathway | 25 | 5 | 1.91 | 0.0452