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Table 1 Summary of co-expression modules associated with neuronal differentiation and depolarization, and TS mutation

From: Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

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
  1. The top five connected genes ranked by kME and the top three enriched GO terms are listed for each module. Modules are labeled if they were preserved in independent in vivo and in vitro expression data sets [41],[42] according to module preservation analysis [40] (Methods).
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Genome Medicine

ISSN: 1756-994X

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