Table 1.
Statistical analysis details
| Figure | Assay performed | Parameter | Comparison WT vs HT |
Descriptive Statistics |
Statistical Analysis |
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|---|---|---|---|---|---|---|---|---|---|---|---|
| Independent variables | n | Average | Error (SE or SD) | Statistical test | F | DF | ANOVA p values | Significance | |||
| 1C | Fluorescence imaging | GFP intensity, AFU | GFP | GFP = 7 coverslips | 7088 | 338.5 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 24.63 | 34 | p < 0.0001 | p = 0.9976 for GFP-Pyk2 vs GFP-Pyk2 & PF719 |
| GFP-Pyk2 | GFP-Pyk2 = 7 coverslips | 3814 | 299.8 (SE) | p = 0.9521 for GFP-Pyk2 vs GFP-Pyk2-K457A | |||||||
| GFP-Pyk2 & PF-719 | GFP-Pyk2 & PF-719 = 7 coverslips | 3680 | 341.4 (SE) | p = 0.0003 for GFP-Pyk2 vs GFP-Pyk2 & PF719 | |||||||
| GFP-Pyk2-K457A | GFP-Pyk2-K457A = 7 coverslips | 3515 | 163.4 (SE) | p < 0.0001 for GFP-Pyk2 vs GFP-Pyk2 & PF719 | |||||||
| GFP & Pyk2 | GFP & Pyk2 = 7 coverslips | 5104 | 305.6 (SE) | ||||||||
| 1D | Fluorescence imaging | Spine density, μm−1 | GFP | GFP = 7 coverslips | 0.445 | 0.023 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 22.4 | 34 | p < 0.0001 | p < 0.0001 for GFP vs GFP-Pyk2 |
| GFP-Pyk2 | GFP-Pyk2 = 7 coverslips | 0.219 | 0.024 (SE) | p = 0.5611 for GFP vs GFP-Pyk2 & PF719 | |||||||
| GFP-Pyk2 & PF-719 | GFP-Pyk2 & PF-719 = 7 coverslips | 0.392 | 0.035 (SE) | p = 0.9978 for GFP vs GFP-Pyk2-K457A | |||||||
| GFP-Pyk2-K457A | GFP-Pyk2-K457A = 7 coverslips | 0.435 | 0.016 (SE) | p < 0.0001 for GFP vs GFP & Pyk2 | |||||||
| GFP & Pyk2 | GFP & Pyk2 = 7 coverslips | 0.202 | 0.021 (SE) | p = 0.0003 for GFP-Pyk2 vs GFP-Pyk2 & PF719 | |||||||
| p < 0.0001 for GFP-Pyk2 vs GFP-Pyk2-K457A | |||||||||||
| 3B | Fluorescence imaging and colocalization test | Merged area, % | GFP & RFP-Graf1c | GFP & RFP-Graf1c = 11 images | 20.03 | 8.255 (SD) | One-way ANOVA; Turkey's multiple-comparisons test | 64.96 | 42 | p < 0.0001 | p < 0.0001 for GFP & RFP-Graf1c vs GFP-Pyk2 & RFP-Graf1c |
| GFP-Pyk2 & RFP-Graf1c | GFP-Pyk2 & RFP-Graf1c = 12 images | 86.76 | 18.02 (SD) | p = 0.1656 for GFP & RFP-Graf1c vs GFP-PXXP2mut & RFP-Grf1c | |||||||
| GFP-PXXP2mut & RFP-Graf1c | GFP-PXXP2mut & RFP-Graf1c = 10 images | 32.81 | 11.4 (SD) | ||||||||
| GFP-PSD95 & RFP-Graf1c | GFP-PSD95 & RFP-Graf1c = 10 images | 80.99 | 15 (SD) | ||||||||
| 4B | Western blotting | Graf1c/actin ratio, normalized by control | Control | Control = 5 experiments | 1 | 0 (SD) | Student's two tailed t test | p = 0.0007 for Control vs Graf1 shRNA | |||
| Graf1 shRNA | Graf1 shRNA = 5 experiements | 0.579 | 0.1753 (SD) | ||||||||
| 4D | ICC | Pyk2 intensity in synapse, normalized to U6 Control | Control = 22 images | 1 | 0.1035 (SE) | Student's two tailed t test | p = 0.035 for Control vs Graf1 shRNA | ||||
| Graf1 shRNA = 21 images | 0.736 | 0.0597 (SE) | |||||||||
| Pyk2 intensity in ex-synapse, normalized to U6 Control | Control = 22 images | 1 | 0.0754 (SE) | Student's two tailed t test | p = 0.2593 for Control vs Graf1 shRNA | ||||||
| Graf1 shRNA = 21 images | 1.072 | 0.0781 (SE) | |||||||||
| PSD-95 puncta # in GFP area, normalized to U6 Control | Control = 22 images | 1 | 0.075 (SE) | Student's two tailed t test | p = 0.9549 for Control vs Graf1 shRNA | ||||||
| Graf1 shRNA = 21 images | 0.739 | 0.0668 (SE) | |||||||||
| 4G | ICC | Pyk2 intensity in PSD-95 area, normalized to GFP Control | GFP = 19 images | 1 | 0.1209 (SE) | Student's two tailed t test | p = 0.0478 for GFP vs GFP-PRD | ||||
| GFP-PRD = 14 images | 0.689 | 0.0607 (SE) | |||||||||
| 5B | ICC | Pyk2 intensity in PSD-95 puncta, normalized by Veh | 1 h | Veh = 11 coverslips | 1 | 0.1133 (SE) | Student's two tailed t test | p = 0.7810 for Veh vs Aβo | |||
| Aβo = 10 coverslips | 1.042 | 0.0958 (SE) | |||||||||
| 6 h | Veh = 10 coverslips | 1 | 0.0798 (SE) | Student's two tailed t test | p = 0.3157 for Veh vs Aβo | ||||||
| Aβo = 9 coverslips | 1.153 | 0.1286 (SE) | |||||||||
| 24 h | Veh = 9 coverslips | 1 | 0.1118 (SE) | Student's two tailed t test | p = 0.0352 for Veh vs Aβo | ||||||
| Aβo = 10 coverslips | 1.284 | 0.0612 (SE) | |||||||||
| 5C | ICC | PSD-95 puncta # /Pyk2 intensity, normalized by Veh | 1 h | Veh = 11 coverslips | 1 | 0.0553 (SE) | Student's two tailed t test | p = 0.7969 for Veh vs Aβo | |||
| Aβo = 10 coverslips | 1.031 | 0.1098 (SE) | |||||||||
| 6 h | Veh = 10 coverslips | 1 | 0.0533 (SE) | Student's two tailed t test | p = 0.4203 for Veh vs Aβo | ||||||
| Aβo = 9 coverslips | 0.901 | 0.1107 (SE) | |||||||||
| 24 h | Veh = 9 coverslips | 1 | 0.0704 (SE) | Student's two tailed t test | p = 0.0352 for Veh vs Aβo | ||||||
| Aβo = 10 coverslips | 0.815 | 0.0493 (SE) | |||||||||
| 5E | Western blotting | Protein / PSD-95 ratio at 6 mo, normalized by WT | Graf1c/ PSD-95 | WT = 6 mice | 1 | 0.0977 (SD) | Student's two tailed t test | p = 0.0281 for WT vs APP/PS1 | |||
| APP/PS1 = 6 mice | 1.168 | 0.1276 (SD) | |||||||||
| Pyk2/PSD-95 | WT = 6 mice | 1 | 0.2251 (SD) | Student's two tailed t test | p = 0.9793 for WT vs APP/PS1 | ||||||
| APP/PS1 = 6 mice | 1.003 | 0.1081 (SD) | |||||||||
| Fyn/PSD-95 | WT = 6 mice | 1 | 0.2381 (SD) | Student's two tailed t test | p = 0.7231 for WT vs APP/PS1 | ||||||
| APP/PS1 = 6 mice | 0.9489 | 0.2479 (SD) | |||||||||
| 5G | Western blotting | Protein/PSD-95 ratio at 9 mo, normalized by WT | Graf1c/ PSD-95 | Total_WT = 5 mice | 1 | 0.1085 (SD) | |||||
| Total_APP/PS1 = 5 mice | 1.033 | 0.0789 (SD) | |||||||||
| PSD_WT = 5 mice | 1 | 0.0595 (SD) | Student's two tailed t test | p = 0.0004 for WT vs APP/PS1 | |||||||
| PSD_APP/PS1 = 5 mice | 1.197 | 0.0458 (SD) | |||||||||
| Pyk2/PSD-95 | Total_WT = 5 mice | 1 | 0.1698 (SD) | ||||||||
| Total_APP/PS1 = 5 mice | 0.984 | 0.0794 (SD) | |||||||||
| PSD_WT = 5 mice | 1 | 0.2054 (SD) | Student's two tailed t test | p = 0.0022 for WT vs APP/PS1 | |||||||
| PSD_APP/PS1 = 5 mice | 1.565 | 0.1971 (SD) | |||||||||
| Fyn / PSD-95 | Total_WT = 5 mice | 1 | 0.1317 (SD) | ||||||||
| Total_APP/PS1 = 5 mice | 1.071 | 0.0856 (SD) | |||||||||
| PSD_WT = 5 mice | 1 | 0.1182 (SD) | Student's two tailed t test | p = 0.5068 for WT vs APP/PS1 | |||||||
| PSD_APP/PS1 = 5 mice | 1.071 | 0.1965 (SD) | |||||||||
| 5I | Western Blotting | Protein/PSD-95 ratio at 13 mo, normalized by WT | Graf1c / PSD-95 | PSD_WT = 6 mice | 1 | 0.0419 (SD) | Student's two tailed t test | p = 0.0411 for WT vs APP/PS1 | |||
| PSD_APP/PS1 = 6 mice | 1.143 | 0.0445(SD) | |||||||||
| Pyk2 / PSD-95 | PSD_WT = 6 mice | 1 | 0.0442 (SD) | Student's two tailed t test | p = 0.0128 for WT vs APP/PS1 | ||||||
| PSD_APP/PS1 = 6 mice | 1.326 | 0.0981 (SD) | |||||||||
| Fyn / PSD-95 | PSD_WT = 6 mice | 1 | 0.0489 (SD) | Student's two tailed t test | p = 0.9337for WT vs APP/PS1 | ||||||
| PSD_APP/PS1 = 6 mice | 1.009 | 0.088 (SD) | |||||||||
| 5J | PLISA | ng Aβo, ng/tissue, g | WT, 3 mo | WT = 6 mice | 0.135 | 0.1343 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 19.23 | 35 | p < 0.0001 | p < 0.0001 for APP/PS1 3 mo vs APP/PS1 12 mo |
| APP/PS1, 3 mo | APP/PS1 = 6 mice | 0.4194 | 0.2721 (SE) | p < 0.0001 for APP/PS1 6 mo vs APP/PS1 12 mo | |||||||
| APP/PS1, 6 mo | APP/PS1 = 6 mice | 1.237 | 0.6306 (SE) | p < 0.0001 for APP/PS1 9 mo vs APP/PS1 12 mo | |||||||
| APP/PS1, 9 mo | APP/PS1 = 6 mice | 6.008 | 2.126 (SE) | ||||||||
| WT, 12 mo | APP/PS1 = 6 mice | 0.354 | 0.0897 (SE) | ||||||||
| APP/PS1, 12 mo | APP/PS1 = 6 mice | 35.43 | 7.478 (SE) | ||||||||
| 5K | IHC | Thioflavin S, % area | WT, 3 mo | WT = 8 mice | 0.0001279 | 8.331e−005 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 34.01 | 46 | p < 0.0001 | p < 0.0001 for APP/PS1 3 mo vs APP/PS1 12 mo |
| APP/PS1, 3 mo mo | APP/PS1 = 8 mice | 0.0005608 | 0.0002712 (SE) | p < 0.0001 for APP/PS1 6 mo vs APP/PS1 12 mo | |||||||
| APP/PS1, 6 mo | APP/PS1 = 8 mice | 0.07512 | 0.02726 (SE) | p < 0.0001 for APP/PS1 9 mo vs APP/PS1 12 mo | |||||||
| APP/PS1, 9 mo | APP/PS1 = 8 mice | 0.573 | 0.1102 (SE) | ||||||||
| WT, 12 mo | APP/PS1 = 7 mice | 0.003523 | 0.00183 (SE) | ||||||||
| APP/PS1, 12 mo | APP/PS1 = 8 mice | 1.436 | 0.2099 (SE) | ||||||||
| 5L | IHC | PSD-95, % area | 12 mo | WT = 7 mice | 4.19 | 0.5074 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 1.666 | 62 | p = 0.1368 | p = 0.0389 for WT vs APP/PS1 |
| APP/PS1 = 8 mice | 1.331 | 0.3533 (SE) | |||||||||
| 6B | In vitro GTP hydrolysis assay | GTP hydrolysis, normalized by RhoA only | Rho | RhoA = 8 experiments | 1 | 0 (SD) | One-way ANOVA; Turkey's multiple-comparisons test | 11.92 | 39 | p < 0.0001 | p = 0.0028 for RhoA & Graf1c vs RhoA, Graf1c & GFP-Pyk2 |
| RhoA, Graf1c | RhoA, Graf1c = 8 experiments | 2.134 | 0.5146 (SD) | p = 0.3415 for RhoA & Graf1c vs RhoA, Graf1c & GFP-K457A | |||||||
| RhoA, GFP-Pyk2, Graf1c | RhoA, GFP-Pyk2, Graf1c = 8 experiments | 1.411 | 0.3605 (SD) | p = 0.6208 for RhoA & Graf1c vs RhoA, Graf1c & GFP-PXXP2mut | |||||||
| RhoA, GFP-K457A, Graf1c | RhoA, GFP-K457A, Graf1c = 8 experiments | 1.791 | 0.2888 (SD) | ||||||||
| RhoA, GFP-PXXP2mut, Graf1c | RhoA, GFP-PXXP2mut, Graf1c = 8 experiments | 1.877 | 0.4246 (SD) | ||||||||
| 6D | RBD pull-down assay | RhoA-GTP/ total RhoA, normalized by WT | RhoA | RhoA = 3 experiments | 1 | 0 (SD) | One-way ANOVA; Turkey's multiple- comparisons test | 23.59 | 17 | p < 0.0001 | p = 0.0089 RhoA vs RhoA & GFP-Pyk2 |
| RhoA & GFP-Pyk2 | RhoA & GFP-Pyk2 = 3 experiments | 1.476 | 0.1363 (SD) | p = 0.0155 RhoA vs RhoA & Graf1c | |||||||
| RhoA & Graf1c | RhoA & Graf1c = 3 experiments | 0.559 | 0.0917 (SD) | p = 0.0018 RhoA & Graf1c vs RhoA, GFP-Pyk2, Graf1c | |||||||
| RhoA, GFP-Pyk2, Graf1c | RhoA, GFP-Pyk2, Graf1c = 3 experiments | 1.142 | 0.1307 (SD) | p > 0.0001 RhoA & Graf1c vs RhoA, GFP-K457A, Graf1c | |||||||
| RhoA, GFP-K457A, Graf1c | RhoA, GFP-K457A, Graf1c = 3 experiments | 0.563 | 0.1812 (SD) | p = 0.9703 RhoA & Graf1c vs RhoA, GFP-PXXP2mut, Graf1c | |||||||
| RhoA, GFP-PXXP2mut, Graf1c | RhoA, GFP-PXXP2mut, Graf1c = 3 experiments | 0.641 | 0.1713 (SD) | ||||||||
| 7B | RBD pull-down assay | RhoA-GTP/ total RhoA, normalized by WT | WT | Veh = 4 experiments | 1 | 0.1474 (SD) | One-way ANOVA; Turkey's multiple- comparisons test | 15.53 | 15 | p = 0.0002 | p = 0.0075 WT veh vs WT Aβo |
| Aβo = 4 experiments | 1.651 | 0.3115 (SD) | |||||||||
| Pyk2−/− | Veh = 4 experiments | 0.715 | 0.2195 (SD) | p = 0.9985 Pyk2−/− veh vs Pyk2−/− Aβo | |||||||
| Aβo = 4 experiments | 0.689 | 0.1985 (SD) | |||||||||
| 7D | RBD pull-down assay | RhoA-GTP/ total RhoA, normalized by WT | 6 mo | WT = 6 mice | 1 | 0.5115 (SD) | Student's two tailed t test | p = 0.9534 for WT vs APP/PS1 | |||
| APP/PS1 = 6 mice | 0.986 | 0.1899 (SD) | |||||||||
| 9 mo | WT = 6 mice | 1 | 0.1688 (SD) | Student's two tailed t test | p = 0.0027 for WT vs APP/PS1 | ||||||
| APP/PS1 = 6 mice | 2.105 | 0.6613 (SD) | |||||||||
| 13 mo | WT = 6 mice | 1 | 0.3357 (SD) | Student's two tailed t test | p < 0.0001 for WT vs APP/PS1 | ||||||
| APP/PS1 = 6 mice | 2.828 | 0.568 (SD) | |||||||||
| 8B | Fluorescence imaging and Spine density | Spine density, μm−1 | GFP | GFP = 7 coverslips | 0.483 | 0.0152 (SE) | One-way ANOVA; Turkey's multiple- comparisons test | 11.48 | 48 | p < 0.0001 | p = 0.4065for GFP vs GFP & Y27632 |
| GFP & Y27632 | GFP & Y27632 = 6 coverslips | 0.412 | 0.0253 (SE) | p = 0.6567 for GFP vs GFP & RhoA-T19N | |||||||
| GFP & RhoA-T19N | GFP & RhoA-T19N = 6 coverslips | 0.425 | 0.0311 (SE) | p < 0.0001 for GFP vs GFP-Pyk2 | |||||||
| GFP-Pyk2 | GFP-Pyk2 = 6 coverslips | 0.213 | 0.0254 (SE) | p < 0.0001 for GFP-Pyk2 vs GFP-Pyk2 & Y27632 | |||||||
| GFP-Pyk2 & Y27632 | GFP-Pyk2 & Y27632 = 7 coverslips | 0.422 | 0.0279 (SE) | p < 0.0001 for GFP-Pyk2 vs GFP-Pyk2 & RhoAT19N | |||||||
| GFP-Pyk2 & RhoA-T19N | GFP-Pyk2 & RhoA-T19N = 4 coverslips | 0.43 | 0.0302 (SE) | p < 0.0001 for GFP-Pyk2 vs GFP-Pyk2 & Graf1c | |||||||
| GFP-Pyk2 & Graf1c | GFP-Pyk2 & RhoA-T19N = 6 coverslips | 0.447 | 0.0197 (SE) | p = 0.9117 for GFP vs GFP-PXXP2mut | |||||||
| GFP-PXXP2mut | GFP-PXXP2mut = 7 coverslips | 0.423 | 0.0164 (SE) | ||||||||
| 8D | Fluorescence imaging and Spine density | Spine density, μm−1 | Control | Control = 8 coverslips | 0.466 | 0.0165 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 23.81 | 22 | p < 0.0001 | p < 0.0001 for Control vs Graf1 shRNA |
| Graf1 shRNA | Graf1 shRNA = 5 coverslips | 0.234 | 0.0223 (SE) | p = 0.0006for Graf1 shRNA vs Graf1 shRNA & Y27632 | |||||||
| Graf1 shRNA & Y27632 | Graf1 shRNA & Y27632 = 5 coverslips | 0.391 | 0.0227 (SE) | p < 0.0001 for Graf1 shRNA vs Graf1 shRNA & RhoA-T19N | |||||||
| Graf1 shRNA & RhoA-T19N | Graf1 shRNA & RhoA-T19N = 5 coverslips | 0.456 | 0.0269 (SE) | ||||||||
| 9B | Live fluorescence imaging spine motility | Changed area, min−1, % | WT | Veh = 16 coverslips | 26.81 | 0.943 (SE) | Student's two tailed t test | p < 0.0001 for Veh vs Aβo | |||
| Aβo = 14 coverslips | 20.39 | 0.9693 (SE) | |||||||||
| Pyk2−/− | Veh = 14 coverslips | 32.65 | 1.562 (SE) | Student's two tailed t test | p = 0.6913 for Veh vs Aβo | ||||||
| Aβo = 14 coverslips | 31.82 | 1.348 (SE) | |||||||||
| WT & PF-719 | Veh = 17 coverslips | 32.21 | 1.134 (SE) | Student's two tailed t test | p = 0.9965 for Veh vs Aβo | ||||||
| Aβo = 16 coverslips | 32.21 | 1.144 (SE) | |||||||||
| WT & Pyk2-PRD | Veh = 6 coverslips | 30.31 | 4.104 (SE) | Student's two tailed t test | p = 0.8334 for Veh vs Aβo | ||||||
| Aβo = 6 coverslips | 29.19 | 3.162 (SE) | |||||||||
| WT & Y27632 | Veh = 15 coverslips | 33.21 | 1.578 (SE) | Student's two tailed t test | p = 0.7427 for Veh vs Aβo | ||||||
| Aβo = 11 coverslips | 32.38 | 1.945 (SE) | |||||||||
| 9D | Live fluorescence imaging Spine motility | Changed area, min−1, % | Con | Con = 6 coverslips | 28.15 | 1.299 (SE) | Student's two tailed t test | p < 0.0001 for Con vs CytoD | |||
| CytoD | CytoD = 6 coverslips | 9.37 | 0.806 (SE) | ||||||||
| 10B | Fluorescence imaging and Spine density | Spine density, μm−1 | WT | Con = 8 coverslips | 0.447 | 0.0233(SE) | One-way ANOVA; Turkey's multiple-comparisons test | 6.43 | 37 | p = 0.0006 | p = 0.0034 for Con vs Aβo 4d |
| Veh 6 h = 7 coverslips | 0.456 | 0.0198 (SE) | p = 0.0023 for Veh 4d vs Aβo 4d | ||||||||
| Aβo 6 h = 7 coverslips | 0.402 | 0.0203 (SE) | |||||||||
| Veh 4d = 8 coverslips | 0.455 | 0.0248 (SE) | |||||||||
| Aβo 4d = 8 coverslips | 0.333 | 0.0163 (SE) | |||||||||
| 10D | Fluorescence imaging & Spine density | Spine density, μm−1 | Pyk2−/− | Control = 8 coverslips | 0.439 | 0.0119 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 0.2701 | 39 | p = 0.8952 | p = 0.997 for Veh 4d vs Aβo 4d |
| Veh 6 h = 8 coverslips | 0.456 | 0.0228 (SE) | |||||||||
| Aβo 6 h = 8 coverslips | 0.429 | 0.0211 (SE) | |||||||||
| Veh 4d = 8 coverslips | 0.454 | 0.0282 (SE) | |||||||||
| Aβo 4d = 8 coverslips | 0.44 | 0.0203 (SE) | |||||||||
| 10F | Fluorescence imaging & Spine density | Spine density, μm−1 | PF-719 | Con = 8 coverslips | 0.442 | 0.0102 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 0.3202 | 23 | p = 0.7295 | p = 0.7998 for Veh 4d vs Aβo 4d |
| Veh 4d = 8 coverslips | 0.44 | 0.0204 (SE) | |||||||||
| Aβo 4d = 8 coverslips | 0.426 | 0.0137 (SE) | |||||||||
| Pyk2-PRD | Con = 5 coverslips | 0.44 | 0.0238 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 0.6194 | 14 | p = 0.5546 | p = 0.7966 for Veh 4d vs Aβo 4d | |||
| Veh 4d = 5 coverslips | 0.427 | 0.0179 (SE) | |||||||||
| Aβo 4d = 5 coverslips | 0.409 | 0.018 (SE) | |||||||||
| RhoA-T19N | Con = 5 coverslips | 0.425 | 0.0246 (SE) | One-way ANOVA; Turkey's multiple-comparisons test | 0.4549 | 14 | p = 0.6450 | p = 0.7974 for Veh 4d vs Aβo 4d | |||
| Veh 4d = 5 coverslips | 0.458 | 0.027 (SE) | |||||||||
| Aβo 4d = 5 coverslips | 0.435 | 0.0234 (SE) | |||||||||
This table delineates the numerical values, replicates, variance, and statistical tests for the data presented in the indicated figures.