TABLE 2.
Pathways identified as significantly enriched for both mRNA changes (a total of 1597 identified) and phosphoproteomic changes (a total of 22 identified) in VHIPP of old Pde11a KO vs WT mice
| #Term ID | Term description | Background gene count | RNA sequencing pathway analyses results | Phosphoproteomics pathway analyses | ||||
|---|---|---|---|---|---|---|---|---|
| observed gene count | strength | FDR‐p | observed gene count | strength | FDR‐p | |||
| KEGG Pathways | ||||||||
| mmu04020 | Calcium signaling pathway | 180 | 37 | 0.45 | 9.17E−06 | 4 | 1.35 | 0.001 |
| mmu04723 | Retrograde endocannabinoid signaling | 145 | 26 | 0.39 | 0.00097 | 4 | 1.44 | 0.001 |
| mmu04724 | Glutamatergic synapse | 113 | 23 | 0.45 | 0.00067 | 3 | 1.42 | 0.0035 |
| mmu04921 | Oxytocin signaling pathway | 149 | 20 | 0.27 | 0.049 | 3 | 1.3 | 0.0067 |
| mmu04022 | cGMP−PKG signaling pathway | 164 | 32 | 0.43 | 7.29E−05 | 3 | 1.26 | 0.0079 |
| mmu05010 | Alzheimer's disease | 167 | 22 | 0.26 | 0.0454 | 3 | 1.26 | 0.0079 |
| mmu04971 | Gastric acid secretion | 72 | 12 | 0.36 | 0.049 | 2 | 1.44 | 0.0169 |
| mmu04727 | GABAergic synapse | 87 | 19 | 0.48 | 0.00097 | 2 | 1.36 | 0.0211 |
| mmu05032 | Morphine addiction | 91 | 26 | 0.6 | 4.95E−06 | 2 | 1.34 | 0.0219 |
| mmu04713 | Circadian entrainment | 95 | 26 | 0.58 | 7.62E−06 | 2 | 1.32 | 0.0227 |
| mmu04725 | Cholinergic synapse | 112 | 24 | 0.47 | 0.00025 | 2 | 1.25 | 0.0241 |
| mmu05225 | Hepatocellular carcinoma | 168 | 23 | 0.28 | 0.0285 | 2 | 1.08 | 0.0382 |
| mmu04360 | Axon guidance | 174 | 33 | 0.42 | 7.65E−05 | 2 | 1.06 | 0.0395 |
| GO Processes | ||||||||
| GO:0050896 | Response to stimulus | 6616 | 664 | 0.14 | 7.61E−19 | 17 | 0.41 | 0.0034 |
| GO:0010243 | Response to organonitrogen compound | 867 | 105 | 0.22 | 3.86E−05 | 7 | 0.91 | 0.0052 |
| GO:0006950 | Response to stress | 2899 | 248 | 0.07 | 0.043 | 11 | 0.58 | 0.0072 |
| GO:0051049 | Regulation of transport | 1782 | 202 | 0.19 | 9.30E−08 | 9 | 0.7 | 0.0072 |
| GO:0009987 | Cellular process | 12459 | 1138 | 0.1 | 6.33E−29 | 21 | 0.23 | 0.0093 |
| GO:0072347 | Response to anesthetic | 81 | 14 | 0.38 | 0.0441 | 3 | 1.57 | 0.01 |
| GO:0010035 | Response to inorganic substance | 505 | 61 | 0.22 | 0.0035 | 5 | 1 | 0.0118 |
| GO:0043279 | Response to alkaloid | 115 | 18 | 0.33 | 0.0376 | 3 | 1.42 | 0.0182 |
| GO:0007268 | Chemical synaptic transmission | 321 | 55 | 0.37 | 2.54E−06 | 4 | 1.1 | 0.0183 |
| GO:0010038 | Response to metal ion | 344 | 42 | 0.23 | 0.0193 | 4 | 1.07 | 0.0183 |
| GO:0032501 | Multicellular organismal process | 5888 | 643 | 0.18 | 6.03E−27 | 14 | 0.38 | 0.0183 |
| GO:0042493 | Response to drug | 926 | 114 | 0.23 | 8.11E−06 | 6 | 0.81 | 0.0183 |
| GO:0051128 | Regulation of cellular component organization | 2337 | 272 | 0.21 | 7.00E−12 | 9 | 0.59 | 0.0183 |
| GO Component | ||||||||
| GO:0120025 | Plasma membrane bounded cell projection | 2172 | 273 | 0.24 | 1.22E−15 | 12 | 0.74 | 2.11E−05 |
| GO:0043005 | Neuron projection | 1429 | 207 | 0.3 | 4.05E−17 | 10 | 0.85 | 2.11E−05 |
| GO:0005737 | Cytoplasm | 9909 | 858 | 0.08 | 3.08E−10 | 21 | 0.33 | 2.54E−05 |
| GO:0008021 | Synaptic vesicle | 183 | 24 | 0.26 | 0.0465 | 5 | 1.44 | 3.27E−05 |
| GO:0045202 | Synapse | 968 | 150 | 0.33 | 2.44E−14 | 8 | 0.92 | 6.43E−05 |
| GO:0005622 | Intracellular | 12,462 | 1099 | 0.09 | 6.33E−20 | 22 | 0.25 | 7.08E−05 |
| GO:0030425 | Dendrite | 694 | 117 | 0.37 | 2.56E−13 | 7 | 1 | 7.08E−05 |
| GO:0098793 | Presynapse | 429 | 60 | 0.29 | 9.86E−05 | 6 | 1.15 | 7.08E−05 |
| GO:0032991 | Protein−containing complex | 4701 | 479 | 0.15 | 2.56E−13 | 14 | 0.47 | 0.00023 |
| GO:0005829 | Cytosol | 3326 | 283 | 0.07 | 0.0249 | 12 | 0.56 | 0.00023 |
| GO:0098796 | Membrane protein complex | 1009 | 119 | 0.21 | 1.56E−05 | 7 | 0.84 | 0.00035 |
| GO:0005623 | Cell | 14,044 | 1233 | 0.08 | 1.32E−26 | 22 | 0.2 | 0.00041 |
| GO:0030424 | Axon | 712 | 123 | 0.38 | 1.48E−14 | 6 | 0.93 | 0.00044 |
Note: All KEGG pathways shown, but only top 13 pathways shown for other classifications for sake of space (sorted by phosphoproteomic FDR‐p value). See Tables S2 and S3 for full list of pathways identified by both studies. See Appendix S4 and Appendix S5 for list of individual genes/proteins identified and all pathways identified by each study.