Table 1 Summary of co-expression modules associated with neuronal differentiation and depolarization, and TS mutation
Module color | Trait association (FDR <0.05) | Preservation | Top enriched GOs | Top 5 connected genes by kME | |||
|---|---|---|---|---|---|---|---|
Differentiation | Depolarization | TS mutation | In vivo | In vitro | |||
Green yellow | ↑ | ↑ |  |  |  | Mammary gland epithelium development, midbrain - hindbrain boundary development, hemopoietic stem cell proliferation | LMX1A, RSPO3, WLS, TM4SF1, ATF3 |
Turquoise | ↑ | ↑ |  | Preserved | Preserved | Synapse part, synaptic transmission, neuron projection | SNAP25, C12orf68, MYT1, MAP6, EEF1A2 |
Black | ↑ | ↑ | ↑ |  |  | Nervous system development, nucleobase catabolic process, hydrolase activity | RPS6KA2, ATP9A, KIAA1549L, FAM229B, AKT1 |
Tan | ↑ | ↓ |  |  | Preserved | Mitochondrial membrane part, ribonucleoside triphosphate metabolic process, unfolded protein binding | KIAA0368, ZNF706, SRI, C9orf169, OPA1 |
Cyan | ↑ |  |  | Preserved |  | Skeletal muscle thin filament assembly, platelet-derived growth factor binding, actin-mediated cell contraction | CAV1, SPP1, ME1, SPP1, VSX1 |
Grey60 | ↑ |  |  |  |  | De novo’ post-translational protein folding, mitochondrion, mitochondrial part | TBCE, EBNA1BP2, CCT4, ASPH, AK2 |
Midnight blue | ↓ | ↑ |  |  |  | Cell morphogenesis involved in differentiation, C21-steroid hormone metabolic process, positive regulation of fat cell differentiation | TPD52L1, GJA1, BMP2, IL17RD, KRT15 |
Yellow | ↓ | ↑ |  | Preserved |  | Nuclear body, positive regulation of cell growth, Golgi vesicle transport | MRPS6, PCID2, PPP6C, GBA2, SETD4 |
Brown | ↓ | ↓ |  | Preserved | Preserved | Intracellular organelle lumen, oxidation-reduction process, NADH dehydrogenase complex | DOCK1, COMMD4, STRADB, SLC16A9, ORC3 |
Blue | ↓ |  |  | Preserved | Preserved | Cell cycle phase, cell division, nuclear division | NIF3L1, LIN28A, TEX10, AMMECR1, NCAPG |
Green |  | ↑ |  |  | Preserved | Vesicle coating, positive regulation of I-kappaB kinase/NF-kappaB cascade, autophagy | NUP98, DNAJA1, DHX37, ETNK1, CGGBP1 |
Red |  | ↓ | ↑ | Preserved | Preserved | Nucleobase metabolic process, nuclease activity, proteasome core complex | USP13, PSMG1, RTN4IP1, PTCD2, PSMG1 |
Light green |  |  | ↑ |  |  | tRNA processing, positive regulation of lipid metabolic process, response to virus | CRYBB2, SNHG5, EXOC1, IFITM2, VAV3 |
Magenta |  |  | ↑ |  |  | Type 1/2 fibroblast growth factor receptor binding; neuron recognition; growth factor activity | CTSF, ZNF626, ZNF521, PLEKHA5, COL4A6 |
Purple |  |  | ↑ | Preserved | Preserved | ncRNA processing; nuclear body, ribonucleoprotein complex biogenesis | RRS1, RRP15, PUS1, NOLC1, ABCE1 |
Light cyan |  |  | ↓ |  |  | Lytic vacuole, integral to organelle membrane | TRAPPC2, ZNF177, HLA-A, ZNF559, RPS26P47 |
Salmon |  |  | ↓ |  |  | Actin filament bundle assembly, regulation of establishment of protein localization in plasma membrane, regulation of type I interferon-mediated signaling pathway | NDUFB11, MSN, UPRT, GPKOW, TSR2 |