DE-3

Supermodule 1068 genes

Neuron projection morphogenesis and synaptic organization

This 1,094-gene module is enriched for genes involved in neuron projection morphogenesis, synapse organization, and cell junction assembly, with genes including APP, BRAF, PTEN, SNCA, and ATM. The module also shows enrichment for GTPase regulator activity, suggesting involvement in Rho/Ras signaling. Knockdown of ARID1A, SMAD3, MIXL1, SMARCC1, and SNAI1 activates this module, while knockdown of SMAD5, SOX11, DR1, HES1, and SOX17 represses it.

Key terms: multicellular organism development neuron projection morphogenesis anatomical structure morphogenesis plasma membrane bounded cell projection morphogenesis cell junction organization Notable genes: APP BRAF PTEN SNCA ATM YAP1 GSK3B FGFR1 Top TFs: ARID1A SMAD5 SOX11 SMAD3 DR1

TF Regulatory Network

Direction indicates the effect of TF knockdown on this module (↑ = KD upregulates; ↓ = KD downregulates).

Perturbation + Binding ↑ ↓

Perturbation only ↑ ↓

Binding only

TF	Dir	NES	#gRNA	padj	Bind	OR

Submodules (50)

Finer-grained co-expression clusters within this supermodule, each with a distinct functional signature.

Submodule	Genes	Notable genes
DE-3.1	38	ABL1 ADAM10 WRN XPO1 PKD2
DE-3.2	34	NF1 MT-ND5 ANK2 ELMO1 DOCK1
DE-3.3	28	PRKN ALCAM FUT8 ACYP2 ZBTB20
DE-3.4	28	MSH3 MTAP AHI1 FANCL NSD3
DE-3.5	27	SNCA NTF3 GRK5 GRHL2 TRPM6
DE-3.6	27	HDAC4 TRPM7 DLG1 PPP3CA NFIB
DE-3.7	26	TNC GPC3 ADGRL3 PRDM5 ARHGAP26
DE-3.8	26	PAK1 CNNM2 ARFGEF2 SCAI TRAK1
DE-3.9	26	TGFBR1 ITGA5 KDM1A NOTCH2 ITGA6
DE-3.10	26	PDGFRA SEMA4D SDC2 SLC12A2 REV1
DE-3.11	25	YAP1 PTK2 MAPK8 ARID1B PUM1
DE-3.12	24	HDAC8 ST6GAL1 CASK ASAP1 KALRN
DE-3.13	22	NCOA2 PBX1 MSI2 KMT2C CLASP1
DE-3.14	21	NCOA1 CBLB WWP1 NEO1 MEIS2
DE-3.15	19	FHIT TIAM1 SMYD3 SOX5 RAD51B
DE-3.16	17	GATA3 TET1 SORL1 COL18A1 GAD1
DE-3.17	17	NSD1 SND1 BIRC6 GRB10 KANK1
DE-3.18	17	GATA4 COL4A1 JAZF1 COL4A2 PDE10A
DE-3.19	17	DPP4 HNF1B MTSS1 PITX1 RGS5
DE-3.20	16	CAMTA1 WIPF1 ADCY1 CLEC2D RTN1
DE-3.21	16	XRCC4 CLCN5 CENPC KIAA0586 DDX10
DE-3.22	15	FGFR1 FN1 PROS1 VCAN FOXP2
DE-3.23	15	ANTXR1 MAP2K5 PIBF1 AP3B1 APLF
DE-3.24	15	BRAF SOS1 TNKS EHMT1 COP1
DE-3.25	15	BCL11A RBPJ AGO1 PDGFC WNK2
DE-3.26	15	ERCC8 PTPRA NEK1 RHBDD1 MYCBP2
DE-3.27	14	RELN ITPR1 LINC00511 PCSK2 ARB2A
DE-3.28	14	MCU THADA RAP1GDS1 TLK1 CDC42BPA
DE-3.29	14	ATR ATF6 TRIM44 MPDZ FBXL4
DE-3.30	13	MDM4 POT1 DCAF1 ZDHHC17 TTI1
DE-3.31	12	ROR1 LAMA1 FNDC3B MCC ADAMTS12
DE-3.32	12	PTPRJ ATG10 HECW2 TBCK LDLRAD3
DE-3.33	12	APP CUX1 PTPRG MAGI1 KLF12
DE-3.34	12	CLIC4 KPNA1 ZMYND11 TRIM71 SCAF4
DE-3.35	12	E2F3 SMC5 MYO3A PKP4 MAST2
DE-3.36	11	FOXP1 COL4A5 ADGRV1 FGF13 COL4A6
DE-3.37	11	PTEN PIK3R1 KDM5B CDK19 BPTF
DE-3.38	11	KITLG LPAR1 ARL13B OVOL2 ARHGAP29
DE-3.39	11	PLD1 SLC39A8 GALC MXI1 CCBE1
DE-3.40	11	TNFRSF19 MARCHF1 STK32A GPR173 PRR5L
DE-3.41	11	MLXIPL HHIP CPS1 EYS PDE11A
DE-3.42	11	NUMA1 FANCM PCNT CEP43 MTBP
DE-3.43	10	PRKCA CDKAL1 LTBP1 DGKH PDE8A
DE-3.44	10	BCR TNFRSF11A SEPTIN9 XYLT1 WLS
DE-3.45	10	KCNQ1OT1 NUMB CTNNA3 BTBD9 FBXL17
DE-3.46	10	PTPN13 SETBP1 UTRN MAPK10 TLN2
DE-3.47	10	BACH1 MAPKAP1 NBAS ZFYVE9 EVI5
DE-3.48	10	SP3 EMSY KIF2A CHD1 PPP3R1
DE-3.49	10	PBRM1 FAT1 ARSB SP4 PAXIP1
DE-3.50	10	F2R TMPRSS2 SOX11 ATP1A1 KIF21A

Module Genes

All genes assigned to this co-expression supermodule.

Gene	Type	Submodule	Publications

Enriched Terms

GO terms and pathway annotations enriched in this gene set (g:Profiler).