Table 1.
List of the 13 over-represented pathways in common between the ConsensusPathDB analyses performed on the three villages.
| Pathway name | Pathway size | Campora | Gioi | Cardile | Genes contained in common | Increased variants in common | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genes contained | p-value | q-value | Genes contained | p-value | q-value | Genes contained | p-value | q-value | ||||
| Axon guidance | 357 | 154 (43.3%) | 2.53E-06 | 1.36E-03 | 126 (35.4%) | 1.97E-05 | 5.97E-03 | 171 (48.0%) | 1.09E-05 | 2.37E-03 | 53 | 18 |
| Beta1 integrin cell surface interactions | 66 | 36 (54.5%) | 1.02E-04 | 2.14E-02 | 32 (48.5%) | 4.98E-05 | 8.98E-03 | 40 (60.6%) | 8.20E-05 | 1.01E-02 | 13 | 3 |
| Collagen biosynthesis and modifying enzymes | 67 | 42 (62.7%) | 1.78E-07 | 1.39E-04 | 31 (46.3%) | 1.94E-04 | 1.75E-02 | 41 (61.2%) | 4.88E-05 | 7.64E-03 | 20 | 5 |
| Collagen chain trimerization | 44 | 33 (75.0%) | 4.57E-09 | 1.73E-05 | 27 (61.4%) | 5.55E-07 | 5.01E-04 | 33 (75.0%) | 3.20E-07 | 1.25E-04 | 20 | 5 |
| Collagen formation | 91 | 53 (58.2%) | 1.56E-07 | 1.39E-04 | 40 (44.0%) | 1.02E-04 | 1.22E-02 | 59 (64.8%) | 6.27E-08 | 3.06E-05 | 26 | 5 |
| ECM-receptor interaction - Homo sapiens | 82 | 44 (53.7%) | 3.10E-05 | 8.36E-03 | 43 (52.4%) | 1.70E-07 | 2.05E-04 | 54 (65.9%) | 1.04E-07 | 4.50E-05 | 20 | 5 |
| Extracellular matrix organization | 293 | 136 (46.4%) | 8.15E-08 | 1.39E-04 | 118 (40.3%) | 1.81E-08 | 6.55E-05 | 165 (56.3%) | 9.41E-12 | 3.68E-08 | 62 | 9 |
| Focal adhesion - Homo sapiens | 199 | 91 (45.7%) | 2.27E-05 | 6.58E-03 | 78 (39.2%) | 1.48E-05 | 5.92E-03 | 105 (52.8%) | 3.78E-06 | 9.86E-04 | 33 | 9 |
| Integrin | 124 | 62 (50.0%) | 1.67E-05 | 5.36E-03 | 59 (47.6%) | 9.41E-08 | 1.70E-04 | 77 (62.1%) | 1.13E-08 | 1.11E-05 | 35 | 7 |
| Protein digestion and absorption - Homo sapiens | 90 | 48 (53.3%) | 1.70E-05 | 5.36E-03 | 41 (45.6%) | 3.05E-05 | 6.94E-03 | 50 (55.6%) | 2.54E-04 | 2.24E-02 | 24 | 6 |
| Stimuli-sensing channels | 102 | 56 (54.9%) | 1.03E-06 | 6.49E-04 | 41 (40.2%) | 8.21E-04 | 4.36E-02 | 60 (58.8%) | 5.92E-06 | 1.45E-03 | 24 | 6 |
| Transport of small molecules | 666 | 265 (39.9%) | 3.17E-06 | 1.50E-03 | 206 (31.0%) | 6.83E-04 | 3.74E-02 | 324 (48.8%) | 1.38E-10 | 2.69E-07 | 86 | 19 |
| Vesicle-mediated transport | 620 | 237 (38.2%) | 2.73E-04 | 4.29E-02 | 205 (33.1%) | 1.18E-05 | 5.92E-03 | 295 (47.6%) | 2.38E-08 | 1.55E-05 | 74 | 22 |
p-values are calculated according to the hypergeometric test based on the number of genes present in both the pathway-based set and input list of genes. q-values represent the p-values corrected for multiple testing using the false discovery rate method. The last two columns in the table represent the genes used as input for the analyses and the increased allele frequency variants located in those genes, that are in common between the three isolates.