DE-1

Supermodule 2011 genes

Ribosomal subunit and translation machinery

This 2012-gene module includes APOE, KRAS, GSTP1, HMGB1, and SOD1, and is highly enriched for ribosomal subunits, ribosomal structure, translation, and protein biosynthesis, with additional enrichment in mitochondrial inner membrane and proton transporter activity. Knockdown of KLF6 and GRHL2 activates this module. Knockdown of CTBP1, SOX11, SOX4, TBX3, and ZNF628 represses this module.

Key terms: translation protein biosynthetic process cytoplasmic translation ribonucleoprotein complex biogenesis ribosome biogenesis Notable genes: APOE KRAS GSTP1 HMGB1 SOD1 PARP1 RAC1 BAX Top TFs: CTBP1 SOX11 KLF6 SOX4 TBX3

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 (57)

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

Submodule	Genes	Notable genes
DE-1.1	61	MIF RACK1 FTH1 EEF1A1 TPT1
DE-1.2	57	DANCR SRY VAMP2 NHERF2 RBM4
DE-1.3	56	KRAS BAK1 SDHB PRKAR1A TSG101
DE-1.4	43	SDHD AIMP1 C1GALT1C1 WDR77 MCFD2
DE-1.5	41	HNRNPK DDX5 YWHAE HNRNPL FXR1
DE-1.6	38	ANXA2 TXN LDHA GSTO1 CLIC1
DE-1.7	35	HMGB1 HSP90AA1 STMN1 HSPA8 RAN
DE-1.8	35	PRMT5 DPAGT1 RUVBL2 KAT8 AAAS
DE-1.9	34	ERCC1 MAP2K2 GLUL TADA3 FKBP1B
DE-1.10	33	ATOX1 ROMO1 RPS27 DSTN SLIRP
DE-1.11	30	TIMP1 GRN KCNQ2 PLTP EGFL7
DE-1.12	25	PPP1CA CSNK2B PHB2 TMBIM6 ADRM1
DE-1.13	25	STUB1 RHOC CD99 BCAP31 CAPNS1
DE-1.14	25	MTDH CXADR USP14 E2F4 BCCIP
DE-1.15	24	PSMD4 GLRX3 DGUOK PSMD1 PSMD2
DE-1.16	24	HSPA5 CALR XBP1 HSP90B1 MYDGF
DE-1.17	24	RTN4 CAMKK2 CBR1 SEPTIN7 MATN3
DE-1.18	22	TFAM KHDRBS1 DKC1 GNL3 GGH
DE-1.19	20	GNAS PGK1 SSBP1 UBE2L3 PUF60
DE-1.20	20	ELAVL1 SMARCB1 GFER RAB8A HYAL2
DE-1.21	19	BAD CD151 CBY1 AGPAT2 USB1
DE-1.22	19	PCBP2 TMEM230 M6PR RNF5 CMTM6
DE-1.23	18	CDC34 RNF126 ITGB1BP1 UPP1 LSM1
DE-1.24	17	PRMT1 PRDX2 ENO1 NDUFA13 RBX1
DE-1.25	17	PRDX3 YWHAB ITGAE MACROH2A1 NDUFV2
DE-1.26	17	BAX CDK4 TUBG1 UBE2M VPS29
DE-1.27	17	GABARAPL2 RAC3 PTP4A2 COX17 BZW1
DE-1.28	17	YY1 PPP2CA HSPA9 DDX21 DHX36
DE-1.29	16	GPX1 GPX4 NEDD8 LAMTOR5 SKP1
DE-1.30	16	ANXA5 GNAI2 MPG RAB25 PDLIM2
DE-1.31	16	GSK3A BRMS1 CLPTM1L ATMIN EFNA2
DE-1.32	16	LMAN1 SPINT1 PYCR1 SEC61A1 CRB3
DE-1.33	14	RAC1 SSB ODC1 PA2G4 ANP32A
DE-1.34	14	CPNE1 SNAP29 PITPNA-AS1 ROGDI ELOF1
DE-1.35	13	GSTP1 CALM1 PPIA CFL1 GAPDH
DE-1.36	13	BSG KRT10 CALM3 EI24 DAD1
DE-1.37	13	ACP1 MIEN1 MPST JTB DNAJC19
DE-1.38	13	VPS35 MED19 NELFE LSR SAMM50
DE-1.39	13	FOXC1 FADD EGLN2 PFN2 PGD
DE-1.40	12	IMPDH2 UXT EIF6 NDUFS2 NDUFS3
DE-1.41	12	FKBP1A RNF7 ECHS1 RAB34 UFC1
DE-1.42	12	NAA10 SDHC CLPP EIF4E2 TRAPPC4
DE-1.43	12	RALA UBE2N GSPT1 UFD1 UBE2D1
DE-1.44	12	GLA IMMT CSTF2 GUSB AK2
DE-1.45	12	WRAP53 DRG2 DMAP1 COQ7 SNUPN
DE-1.46	11	RPLP2 RPL22 RPL34 RPL35A RPS24
DE-1.47	11	SOD1 PDIA3 ITM2B HSD17B10 ADH5
DE-1.48	11	NME1 PABPN1 PRDX4 MTCH2 SMS
DE-1.49	11	LAMP1 COPS6 EIF3D NAXE PSME1
DE-1.50	11	GGCT HAT1 HNRNPF RPA3 NOP56
DE-1.51	11	CYBA RAB11A FOXH1 SUPT4H1 NDUFB9
DE-1.52	11	CETN2 FRG1 TMCO1 NDUFA1 SELENOK
DE-1.53	11	CCKBR PLPPR3 MAGED1 PNKD GSTK1
DE-1.54	11	PARP1 YWHAQ FKBP4 SSRP1 EEF1E1
DE-1.55	10	RHOA HRAS CBS HAX1 ARHGDIA
DE-1.56	10	OTUB1 APH1A MAF1 TUSC2 PTGES2
DE-1.57	10	HNRNPA1 HNRNPC ABCE1 PPP1CC PPID

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).