Table 3.
Summary of most relevant GO terms, pathways and brain lists annotation for relevant modules in frontal cortex (a) and temporal cortex (b)
| FTD gene | MM | 1-q | type | module | sz | G:Profiler Annotation (GO terms & Pathways analyses) | WGCNA – Brain lists |
|---|---|---|---|---|---|---|---|
| a. | |||||||
| MAPT | 0.83 | 0.03 | pure | black | 791 |
BP: Transcription, DNA-templated (p=2.77x10-5); RNA biosynthetic process (p=3.17x10-5); Chromatin modification (p=9.45x10-5) CC: Nuclear lumen (p=2.81x10-13); Histone methyltransferase complex (p=3.2x10-7) MF: Transcription factor binding transcription factor activity (p=6.26x10-6); Nucleic acid binding (p=7.19x10-6)c3v1234 Pathways: Chromatin organization and Chromatin modifying enzymes (p=4.84x10-3ZX) |
Glutamatergic Synaptic Function (CTX) (p=1.36x10-7) |
| GRN | 0.66 | 0.34 | |||||
| HLA-DRA | 0.8 | 0.23 | darkred | 141 |
BP: Immune system process (p=1.39x10-31); Defense response (p=5.23x10-29); Innate immune response (p=2.51x10-19); Adaptive immune response (p=1.71x10-7); Phagocytosis (p=6.2x10-3) CC: MHC class II protein complex (p=1.17x10-7); Lysosome (p=7.69x10-5); Lytic vacuole (p=7.69x10-5) MF: Receptor activity (p=1.88x10-8); Signal transducer activity (p=6.45x10-6) Pathways: Immune system (p=4.8x10-21); Phagosome (p=6.69 x 10-12); Adaptive immune system (p=5.08 x 10-10); Cytokine signaling in immune system (p=2.63 x 10-7); Lysosome (p=4.89 x 10-2) |
Microglia (Type1) (HumanMeta) (p=1.53x10-84) Microglia (Type1) (CTX) (p=7.01x10-31) Up In Frontal Cortex (Early AD) (p=2.96x10-19) |
|
| CTSC | 0.73 | 0.5 | |||||
| TMEM106B | 0.78 | 0.04 | red | 925 |
BP: Cellular protein metabolic process (p=3.84x10-5) CC: Nuclear lumen (p=9.36x10-6); Catalytic complex (p=1.36x10-2) MF: Ligase activity (p=1.96x10-2) Pathways: Chromatin organization (p=1.1x10-2); HATs acetylate histones (p=1.3 x 10-2); HDACs deacetylate histones (p=3.2 x 10-2) |
Protein metabolism (CTX) (p=7.57x10-10) Neuron (CTX) (p=4.83x10-5) Nucleus (HumanMeta) (p=1.09x10-5) Oligodendrocyte probable (Cahoy) (p=2.42x10-5) Brown pyramidal Neurons Layer5/basolateral Amygdala (Sugino/Winden) (p=2.80x10-5) |
|
| C9orf72 | 0.74 | 0.1 | spectrum | purple | 1559 |
BP: Modification-dependent macromolecule catabolic process (p=3.9x10-7); Ubiquitin-dependent protein catabolic process (p=1.08x10-6); Proteolysis involved in cellular protein catabolic process (p=1.72x10-6) CC: Cytoplasm (p=2.95x10-14); Mitochondrion (p=2.4x10-12); Proteasome complex (p=2.81x10-4) MF: Catalytic activity (p=3.55x10-4) Pathways: Protein processing in endoplasmic reticulum (p=1.01x10-5); Mitochondrial translation (p=2.28x10-3) |
Neuron (CTX) (p=8.76x10-27) Neuron (HumanMeta) (p=9.02x10-25) Mitochondrion (p=1.63x10-19) Post Synaptic Density proteins (Bayes) (p=8.73x10-18) |
| VCP | 0.68 | 0.19 | |||||
| UBQLN2 | 0.55 | 0.45 | |||||
| OPTN | 0.59 | 0.38 | |||||
| b. | |||||||
| MAPT | 0.67 | 0.31 | pure | lightyellow | 210 |
BP: Transcription from RNA polymerase II promoter (p=1.23x10-4) CC: Nucleus (p=3.69x10-5) MF: Protein binding (p=2.93x10-4); Transcription factor binding (p=1.42x10-2) Pathways: RNA Polymerase II Transcription Elongation (p=4.21x10-2) |
Glutamatergic Synaptic Function (CTX) (p=3.79x10-5) |
| GRN | 0.56 | 0.51 | cyan | 276 |
CC: intracellular membrane-bounded organelle (p=7.56x10-3) Pathways: Signaling by Wnt (p=7.61x10-3); Lysosome (p=1.21x10-2) |
Glutamatergic Synaptic Function (CTX) (p=9.89x10-8) Mitochondria (HumanMeta) (p=1.74 x10-5) |
|
| HLA-DRA | 0.66 | 0.51 | lightcyan | 250 |
BP: Immune system process (p=1.89x10-37); Defense response (p=1.51x10-32); Phagocytosis (p=1.39x10-5) CC: MHC class II protein complex (p=3.02x10-6); Lysosome (p=5.43x10-5); Lytic vacuole (p=5.43x10-5) MF: Receptor activity (p=4.41x10-10) Pathways: Immune system (p=8x10-22); Phagosome (p=7.2x10-13); Innate immune system (p=1x10-11); Adaptive immune system (p=2.56x10-9) |
Microglia (Type1) (HumanMeta) (p=1.53x10-84) Microglia (Type1) (CTX) (p=1.08x10-30) Up In Frontal Cortex (EarlyAD) (p=7.85x10-19) |
|
| CTSC | 0.69 | 0.47 | |||||
| TMEM106B | 0.86 | 0.01 | darkturquoise | 164 |
CC: Cytoplasm (p=2.8x10-5); Nucleus (p=2.49x10-4) Pathways: Protein processing in endoplasmic reticulum (p=4.86x10-5) |
Nucleus (CTX) (p=3.67x10-9) Metabolism (CTX) (p=3.48x10-5) |
|
| C9orf72 | 0.75 | 0.14 | spectrum | purple | 830 |
BP: Proteolysis involved in cellular protein catabolic process (p=1.81x10-8); Ubiquitin-dependent protein catabolic process (p=3.04x10-8); Protein catabolic process (p=1.87x10-6) CC: Cytoplasm (p=1.28x10-12); Proteasome complex (p=1.16x10-5); Endoplasmic reticulum membrane (p=5.21x10-3) MF: Catalytic activity (p=1.08x10-4) Pathways: Protein processing in endoplasmic reticulum (p=5.25x10-6) |
Neuron (CTX) (p=9.29x10-24) Neuron (HumanMeta) (p=6.96x10-11) Post Synaptic Density proteins (Bayes) (p=4.34x10-5) |
| VCP | 0.71 | 0.24 | |||||
| UBQLN2 | 0.63 | 0.45 | |||||