Table 4 |.
CP risk gene pathway enrichment
| Term names and IDs | Overlap per set | Observed | Expected | FDR | |
|---|---|---|---|---|---|
| Database | |||||
| DAVID | Non-integrin membrane–ECM interactions (R-HSA-3000171) | 10/40 | 10/218 | 40/9,075 | 0.00045 |
| Laminin interactions (R-HSA-3000157) | 8/30 | 8/218 | 30/9,075 | 0.0075 | |
| ECM–receptor interaction (R-HSA-04512) | 12/87 | 12/168 | 87/6,879 | 0.00888 | |
| PANTHER | Non-integrin membrane–ECM interactions (R-HSA-3000171) | 12/59 | 12/447 | 59/20,851 | 6.02 × 10−5 |
| Laminin interactions (R-HSA-3000157) | 8/30 | 8/447 | 30/20,851 | 0.00114 | |
| Signaling by Rho GTPases (R-HSA-194315) | 24/408 | 24/447 | 408/20,851 | 0.00721 | |
| Extracellular matrix organization (R-HSA-1474244) | 20/299 | 20/447 | 299/20,851 | 0.00826 | |
| MSigDB | Non-integrin membrane–ECM interactions (R-HSA-30000171) | 12/59 | 12/439 | 59/38,055 | 5.53 × 10−9 |
| Laminin interactions (R-HSA-30000157) | 8/30 | 8/439 | 30/38,055 | 4.65 × 10−7 | |
| Signaling by Rho GTPases (R-HSA-194315) | 26/450 | 26/439 | 450/38,055 | 2.15 × 10−8 | |
| Extracellular matrix organization (R-HSA-1474244) | 20/301 | 20/439 | 301/38,055 | 1.97 × 10−7 | |
| Biological processes | Cell projection and organization | ||||
| Regulation of cell projection organization (GO:0031344) | 47/695 | 47/447 | 695/20,851 | 1.35 × 10−7 | |
| Positive regulation of cell projection organization (GO:0031346) | 30/395 | 30/447 | 395/20,851 | 1.84 × 10−5 | |
| Positive regulation of neuron projection development (GO:0010976) | 19/294 | 19/447 | 294/20,851 | 0.0087 | |
| Microtubule-based movement | |||||
| Movement of cell or subcellular component (GO:0006928) | 66/1,544 | 66/447 | 1,544/20,851 | 1.22 × 10−4 | |
| Microtubule-based process (GO:0007017) | 32/667 | 32/447 | 667/20,851 | 0.00875 | |
| Microtubule-based movement (GO:0007018) | 18/271 | 18/447 | 271/20,851 | 0.00966 | |
| Cell components | Axonal cell projection | ||||
| Plasma membrane bounded cell projection part (GO:0120025) | 89/2,197 | 89/447 | 2,197/20,851 | 7.15 × 10−6 | |
| Axon (GO:0030424) | 34/641 | 34/447 | 641/20,851 | 0.000882 | |
| Actin-based cell projection (GO:0098858) | 15/214 | 15/447 | 214/20,851 | 0.00898 | |
| Microtubule-associated components | |||||
| Cytoskeleton (GO:0005856) | 82/2,274 | 82/447 | 2,274/20,851 | 0.000894 | |
| Microtubule cytoskeleton (GO:0015630) | 46/1,246 | 46/447 | 1,246/20,851 | 0.0213 | |
| Microtubule associated complex (GO:0005875) | 11/154 | 11/447 | 154/20,851 | 0.0302 | |
| Molecular functions | GTPase activity | ||||
| Small GTPase binding (GO:0031267) | 28/421 | 28/421 | 421/20,851 | 7.98 × 10−5 | |
| Rho GTPase binding (GO:0017048) | 19/145 | 19/447 | 145/20,851 | 9.63 × 10−7 | |
| GTPase regulator activity (GO:0030695) | 18/307 | 18/447 | 307/20,851 | 0.0211 | |
| Actin cytoskeleton regulation | |||||
| Extracellular matrix structural constituent (GO:0005201) | 15/165 | 15/447 | 165/20,851 | 0.00108 | |
| Actin binding (GO:0003779) | 23/443 | 23/447 | 443/20,851 | 0.0207 | |
Key pathways and terms overlapping among DAVID, PANTHER and MSigDB bioinformatics tools. PANTHER GO terms include cell projections, cytoskeleton and Rho GTPase signaling. GO terms were extracted from the total set (Supplementary Datasets 6–15) using hierarchical nesting, or functions that were represented by multiple GO terms. Overlap per set refers to the number of genes overlapping between CP risk genes and a given database term/the total number of genes in the database for that term. FDR = q value (FDR cutoff = 0.05) from two-tailed Fisher and hypergeometric tests. FDR differences are due to differences in tool methodologies.