Table 3 Summary of most relevant GO terms, pathways and brain lists annotation for relevant modules in frontal cortex (a) and temporal cortex (b)

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

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