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

From: Frontotemporal dementia: insights into the biological underpinnings of disease through gene co-expression network analysis

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