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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).