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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).