Name: Endoderm Perturb-Seq Browser
Creator: Huangfu Lab

292 submodules

Submodule	Genes	Notable Genes	Top TF Regulators	Top Enriched Terms
DE-1.1 DE-1	61	MIF RACK1 FTH1 EEF1A1 TPT1	↓TAF10 ↑CTBP1 ↓SOX17	cytosolic ribosome structural constituent of ribosome ribosomal subunit
DE-1.2 DE-1	57	DANCR SRY VAMP2 NHERF2 RBM4	↓ZC3H3 ↓SOX17 ↑ZNF628	—
DE-1.3 DE-1	56	KRAS BAK1 SDHB PRKAR1A TSG101	—	GDP binding guanyl nucleotide binding guanyl ribonucleotide binding
DE-1.4 DE-1	43	SDHD AIMP1 C1GALT1C1 WDR77 MCFD2	—	mitochondrial membrane organelle inner membrane mitochondrial inner membrane
DE-1.5 DE-1	41	HNRNPK DDX5 YWHAE HNRNPL FXR1	↓SOX17 ↓PREB ↓ZC3H3	ribonucleoprotein complex catalytic step 2 spliceosome
DE-1.6 DE-1	38	ANXA2 TXN LDHA GSTO1 CLIC1	↓SOX17	vesicle extracellular vesicle extracellular exosome
DE-1.7 DE-1	35	HMGB1 HSP90AA1 STMN1 HSPA8 RAN	↑SMARCC1 ↓SOX17 ↑CNBP	RNA binding nucleoplasm nucleus
DE-1.8 DE-1	35	PRMT5 DPAGT1 RUVBL2 KAT8 AAAS	↑CTBP1 ↑SOX11 ↓KLF6	protein-containing complex nuclear protein-containing complex ribonucleoprotein complex
DE-1.9 DE-1	34	ERCC1 MAP2K2 GLUL TADA3 FKBP1B	—	—
DE-1.10 DE-1	33	ATOX1 ROMO1 RPS27 DSTN SLIRP	↓ARID1A ↑SOX11 ↑SMAD5	structural constituent of ribosome cytosolic ribosome ribosomal subunit
DE-1.11 DE-1	30	TIMP1 GRN KCNQ2 PLTP EGFL7	↓DNAJC19 ↓SOX17 ↑SOX4	nicotinamide nucleotide biosynthetic process NAD+ biosynthetic process pyridine nucleotide biosynthetic process
DE-1.12 DE-1	25	PPP1CA CSNK2B PHB2 TMBIM6 ADRM1	—	endopeptidase complex peptidase complex proteasome complex
DE-1.13 DE-1	25	STUB1 RHOC CD99 BCAP31 CAPNS1	↓KLF6 ↑SOX4 ↑SOX11	—
DE-1.14 DE-1	25	MTDH CXADR USP14 E2F4 BCCIP	—	—
DE-1.15 DE-1	24	PSMD4 GLRX3 DGUOK PSMD1 PSMD2	↓GATAD2A ↓SOX17 ↓ZC3H3	proteasome complex proteasome regulatory particle proteasome accessory complex
DE-1.16 DE-1	24	HSPA5 CALR XBP1 HSP90B1 MYDGF	↑MYNN	endoplasmic reticulum endoplasmic reticulum lumen response to endoplasmic reticulum stress
DE-1.17 DE-1	24	RTN4 CAMKK2 CBR1 SEPTIN7 MATN3	—	guanyl nucleotide binding ion binding GTP binding
DE-1.18 DE-1	22	TFAM KHDRBS1 DKC1 GNL3 GGH	↓SOX17	RNA binding organelle lumen sno(s)RNA-containing ribonucleoprotein complex
DE-1.19 DE-1	20	GNAS PGK1 SSBP1 UBE2L3 PUF60	—	respiratory chain complex aerobic respiration oxidative phosphorylation
DE-1.20 DE-1	20	ELAVL1 SMARCB1 GFER RAB8A HYAL2	↓ZC3H3	nucleic acid metabolic process RNA metabolic process nucleobase-containing compound metabolic process
DE-1.21 DE-1	19	BAD CD151 CBY1 AGPAT2 USB1	—	acylglycerol O-acyltransferase activity lysophosphatidic acid acyltransferase activity 1-acylglycerol-3-phosphate O-acyltransferase activity
DE-1.22 DE-1	19	PCBP2 TMEM230 M6PR RNF5 CMTM6	—	early endosome endosome
DE-1.23 DE-1	18	CDC34 RNF126 ITGB1BP1 UPP1 LSM1	—	ubiquitin-like protein conjugating enzyme activity ubiquitin conjugating enzyme activity uridine phosphorylase activity
DE-1.24 DE-1	17	PRMT1 PRDX2 ENO1 NDUFA13 RBX1	—	respiratory chain complex catalytic complex cellular respiration
DE-1.25 DE-1	17	PRDX3 YWHAB ITGAE MACROH2A1 NDUFV2	↑PREB	regulation of transcription by RNA polymerase I transcription by RNA polymerase I regulation of transcription of nucleolar large rRNA by RNA polymerase I
DE-1.26 DE-1	17	BAX CDK4 TUBG1 UBE2M VPS29	↓ZC3H3 ↓SOX17 ↑CTBP1	—
DE-1.27 DE-1	17	GABARAPL2 RAC3 PTP4A2 COX17 BZW1	↓SOX17	—
DE-1.28 DE-1	17	YY1 PPP2CA HSPA9 DDX21 DHX36	—	RNA binding nucleic acid binding ribosome biogenesis
DE-1.29 DE-1	16	GPX1 GPX4 NEDD8 LAMTOR5 SKP1	—	phospholipid-hydroperoxide glutathione peroxidase activity lipoxygenase pathway response to selenium ion
DE-1.30 DE-1	16	ANXA5 GNAI2 MPG RAB25 PDLIM2	—	hydrolase activity, hydrolyzing N-glycosyl compounds hydrolase activity, acting on glycosyl bonds alkylbase DNA N-glycosylase activity
DE-1.31 DE-1	16	GSK3A BRMS1 CLPTM1L ATMIN EFNA2	—	—
DE-1.32 DE-1	16	LMAN1 SPINT1 PYCR1 SEC61A1 CRB3	↑SMAD5 ↑DR1	endoplasmic reticulum to Golgi vesicle-mediated transport endoplasmic reticulum Golgi vesicle transport
DE-1.33 DE-1	14	RAC1 SSB ODC1 PA2G4 ANP32A	—	U2-type precatalytic spliceosome precatalytic spliceosome ribonucleoprotein complex
DE-1.34 DE-1	14	CPNE1 SNAP29 PITPNA-AS1 ROGDI ELOF1	—	—
DE-1.35 DE-1	13	GSTP1 CALM1 PPIA CFL1 GAPDH	↑SOX11 ↓SOX17	extracellular exosome extracellular membrane-bounded organelle extracellular organelle
DE-1.36 DE-1	13	BSG KRT10 CALM3 EI24 DAD1	—	—
DE-1.37 DE-1	13	ACP1 MIEN1 MPST JTB DNAJC19	—	3-mercaptopyruvate sulfurtransferase activity pyrimidine nucleotide binding protein-L-histidine N-pros-methyltransferase activity
DE-1.38 DE-1	13	VPS35 MED19 NELFE LSR SAMM50	↓ZC3H3 ↓DNAJC19 ↓SOX17	tricarboxylic acid cycle heteromeric enzyme complex succinate-CoA ligase (GDP-forming) activity succinate-CoA ligase (ADP-forming) activity
DE-1.39 DE-1	13	FOXC1 FADD EGLN2 PFN2 PGD	↓SOX17	regulation of osteoclast proliferation positive regulation of leukocyte proliferation regulation of activation-induced cell death of T cells
DE-1.40 DE-1	12	IMPDH2 UXT EIF6 NDUFS2 NDUFS3	—	mitochondrial membrane mitochondrial envelope organelle inner membrane
DE-1.41 DE-1	12	FKBP1A RNF7 ECHS1 RAB34 UFC1	↓SMAD3	—
DE-1.42 DE-1	12	NAA10 SDHC CLPP EIF4E2 TRAPPC4	↓SOX17 ↓FOXH1	translation initiation factor activity protein-N-terminal-glutamate acetyltransferase activity omega-amidase activity
DE-1.43 DE-1	12	RALA UBE2N GSPT1 UFD1 UBE2D1	—	RNA binding ATPase activator activity GTPase activity
DE-1.44 DE-1	12	GLA IMMT CSTF2 GUSB AK2	—	hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity, acting on glycosyl bonds glycoside catabolic process
DE-1.45 DE-1	12	WRAP53 DRG2 DMAP1 COQ7 SNUPN	—	ubiquinone biosynthesis complex ubiquinone biosynthetic process ubiquinone metabolic process
DE-1.46 DE-1	11	RPLP2 RPL22 RPL34 RPL35A RPS24	↑SOX11	cytosolic ribosome structural constituent of ribosome ribosomal subunit
DE-1.47 DE-1	11	SOD1 PDIA3 ITM2B HSD17B10 ADH5	↓SOX17 ↓FOXH1 ↑SNAI1	oxidoreductase activity, acting on CH-OH group of donors oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity
DE-1.48 DE-1	11	NME1 PABPN1 PRDX4 MTCH2 SMS	—	biogenic amine biosynthetic process amine biosynthetic process biogenic amine metabolic process
DE-1.49 DE-1	11	LAMP1 COPS6 EIF3D NAXE PSME1	↓VEZF1 ↑SMAD4	glyoxylate reductase activity NAD(P)HX epimerase activity glyoxylate reductase (NADPH) activity
DE-1.50 DE-1	11	GGCT HAT1 HNRNPF RPA3 NOP56	—	sno(s)RNA-containing ribonucleoprotein complex phosphoribosylaminoimidazole carboxylase activity phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
DE-1.51 DE-1	11	CYBA RAB11A FOXH1 SUPT4H1 NDUFB9	—	delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity superoxide-generating NAD(P)H oxidase activity basal transcription machinery binding
DE-1.52 DE-1	11	CETN2 FRG1 TMCO1 NDUFA1 SELENOK	↓KLF6 ↑KLF8 ↓SOX17	monoatomic cation transmembrane transporter activity primary active transmembrane transporter activity active monoatomic ion transmembrane transporter activity
DE-1.53 DE-1	11	CCKBR PLPPR3 MAGED1 PNKD GSTK1	—	cholecystokinin receptor activity phosphopantothenate--cysteine ligase activity cholecystokinin receptor binding
DE-1.54 DE-1	11	PARP1 YWHAQ FKBP4 SSRP1 EEF1E1	—	NAD+-protein-histidine ADP-ribosyltransferase activity NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity NAD+-protein-tyrosine ADP-ribosyltransferase activity
DE-1.55 DE-1	10	RHOA HRAS CBS HAX1 ARHGDIA	—	interleukin-1 binding GTPase binding signaling adaptor activity
DE-1.56 DE-1	10	OTUB1 APH1A MAF1 TUSC2 PTGES2	—	mitochondrion deNEDDylase activity oligopeptide binding
DE-1.57 DE-1	10	HNRNPA1 HNRNPC ABCE1 PPP1CC PPID	—	intracellular organelle lumen membrane-enclosed lumen organelle lumen
DE-2.1 DE-2	84	EP300 FBXW7 CREBBP IGF2BP3 LRP6	↑SOX17 ↑ZC3H3 ↑TCEB3	regulation of biological process regulation of cellular process regulation of gene expression
DE-2.2 DE-2	72	TUG1 CSNK1A1 MAT2A SNHG3 KMT2E	↑ZC3H3 ↓ZIC3	—
DE-2.3 DE-2	44	CCM2 PLCG1 STK4 CRY1 VAPB	—	—
DE-2.4 DE-2	39	SPAST KRIT1 NCK1 USP8 KDM5A	↓SOX11	—
DE-2.5 DE-2	30	RB1 LRP5 SMO SKI SSH1	—	negative regulation of osteoblast differentiation
DE-2.6 DE-2	25	FGF1 CEMIP MSRA OSBP2 SZT2	↑ARID1A	—
DE-2.7 DE-2	23	GNAQ IGF2R MRTFA CELF1 ATXN7	↓SOX11	—
DE-2.8 DE-2	20	CTNNB1 ACVR1 DIAPH1 CCDC88A SMURF2	—	BMP receptor activity activin receptor activity, type I activin binding
DE-2.9 DE-2	19	CDK6 CLIP1 EEA1 EPS15 GREM2	—	—
DE-2.10 DE-2	19	TMEM67 PRDM10 IQCK ZNF655 ZNF251	—	—
DE-2.11 DE-2	18	ABCC1 TRAF3 NCOR2 NR2C2 DIDO1	↑SOX11 ↓FOXH1 ↓SMAD4	molecular adaptor activity protein-macromolecule adaptor activity signaling adaptor activity
DE-2.12 DE-2	18	SMARCA4 SMAD7 AXIN1 INO80 MARK2	—	enzyme-substrate adaptor activity ubiquitin-like ligase-substrate adaptor activity I-SMAD binding
DE-2.13 DE-2	18	IRS1 SLC16A4 SENP1 TDP1 KIF7	—	monocarboxylic acid transmembrane transporter activity D-glucose import across plasma membrane positive regulation of D-glucose transmembrane transport
DE-2.14 DE-2	17	ATG5 REV3L BCL2L14 RBMS1 PPP2R3A	—	arginyl-tRNA--protein transferase activity aminoacyltransferase activity methylglutaconyl-CoA hydratase activity
DE-2.15 DE-2	17	POR CRK SOCS6 CLK1 PPP1R10	—	—
DE-2.16 DE-2	17	IL7 GNE NCOA7 LRP2BP SUSD1	—	N-acylmannosamine kinase activity interleukin-7 receptor binding UDP-N-acetylglucosamine 2-epimerase activity
DE-2.17 DE-2	16	STIM1 PDE5A WWP2 DEPDC5 SLC12A6	—	—
DE-2.18 DE-2	16	LYPLAL1 DMGDH RNF13 TTC8 GDPD1	—	lysophospholipase A1 activity phosphatidylcholine lysophospholipase A1 activity A1-type glycerophospholipase activity
DE-2.19 DE-2	15	ITGAV DAPK1 LATS2 EXT1 TEAD1	—	hippo signaling integrin alphav-beta8 complex alphav-beta3 integrin-PKCalpha complex
DE-2.20 DE-2	15	BTD SYNGAP1 SNX1 CPEB3 WDR35	—	metallodipeptidase activity biotinidase activity short-chain 2-methyl fatty acyl-CoA dehydrogenase activity
DE-2.21 DE-2	15	HNF4A PAX2 SLCO2A1 RIPOR2 SMAP2	—	kidney rudiment formation vitamin B6 transport kidney field specification
DE-2.22 DE-2	15	LYN SATB2 PAWR TOX3 LAMC1	—	oxidoreductase activity, acting on the CH-NH2 group of donors, disulfide as acceptor arachidonate-CoA ligase activity chondroitin-glucuronate 5-epimerase activity
DE-2.23 DE-2	14	TOP1 MIR17HG CUL3 YES1 TNPO1	—	nucleocytoplasmic carrier activity ubiquitin-like protein transferase activity ubiquitin-protein transferase activity
DE-2.24 DE-2	14	MCPH1 ATXN10 ENOX2 ELP3 EEFSEC	—	phosphorylase kinase regulator activity diacylglycerol cholinephosphotransferase activity tRNA uridine(34) acetyltransferase activity
DE-2.25 DE-2	13	PTPN11 USP10 MED15 METTL16 AGFG1	—	U6 snRNA 3'-end binding 1-alkyl-2-acetylglycerophosphocholine esterase activity U6 snRNA (adenine-(43)-N(6))-methyltransferase activity
DE-2.26 DE-2	13	HULC CHM UVSSA DHTKD1 D2HGDH	—	(R)-2-hydroxyglutarate dehydrogenase activity 2-oxoadipate dehydrogenase activity alpha-(1->3)-fucosyltransferase activity
DE-2.27 DE-2	13	ROCK1 CREM HIPK1 FNTB KPNA5	—	GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity soluble NSF attachment protein activity glycerol kinase activity
DE-2.28 DE-2	13	TPD52 ITPR3 DAPK2 L2HGDH SYNJ2	—	D-xylulokinase activity selenocysteine lyase activity (S)-2-hydroxyglutarate dehydrogenase activity
DE-2.29 DE-2	12	MAPK14 ADAM9 RPS6KA3 RANBP9 LEMD3	—	positive regulation of syncytium formation by plasma membrane fusion regulation of syncytium formation by plasma membrane fusion response to lipopolysaccharide
DE-2.30 DE-2	12	FAM120C ZNF565 FAM151B-DT ZBTB47-AS1 ENSG00000259986	—	—
DE-2.31 DE-2	12	MAVS GAK PPP1R13B MAPK8IP3 MYO18A	—	carbohydrate:proton symporter activity sucrose:monoatomic cation symporter activity disaccharide transmembrane transporter activity
DE-2.32 DE-2	12	C5 NFATC1 GDF11 LINC00632 IL17RD	—	cytokine activity photoreceptor distal connecting cilium rod photoreceptor outer segment
DE-2.33 DE-2	12	PLXNB1 SEC16A LMAN2L DLGAP4 MAU2	↓FOXH1 ↑VEZF1 ↓SETDB1	Scc2-Scc4 cohesin loading complex COPII-coated ER to Golgi transport vesicle SMC loading complex
DE-2.34 DE-2	11	CNOT2 MYSM1 ZDHHC20 PHF3 MBTD1	—	macromolecule biosynthetic process
DE-2.35 DE-2	11	NCOR1 CUL5 WAPL ORC2 ZNF652	—	X11-like protein binding ATP-dependent protein-DNA unloader activity
DE-2.36 DE-2	11	TNKS2 FOXK1 RAB6A ATG14 MORC3	—	extrinsic component of phagophore assembly site membrane extrinsic component of omegasome membrane axoneme
DE-2.37 DE-2	11	REST STK38 MIA3 UBE2K CLPX	—	UFM1-modified protein reader activity RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding
DE-2.38 DE-2	11	TBK1 DNM1 NFX1 SLCO3A1 SLC10A7	—	—
DE-2.39 DE-2	11	GABBR1 SACS MMP16 RIMS1 DOCK5	—	G protein-coupled GABA receptor complex cell body fiber G protein-coupled receptor heterodimeric complex
DE-2.40 DE-2	10	PIK3CA MTMR3 RC3H1 WDR26 JMY	—	phosphatidylinositol 3-kinase complex, class IB MTREC complex
DE-2.41 DE-2	10	ACACA KDM4B GNA12 GNB1 RAPGEF1	—	heterotrimeric G-protein complex GTPase complex extrinsic component of cytoplasmic side of plasma membrane
DE-2.42 DE-2	10	ADIPOR2 ARID3B SCYL2 ANKFY1 RAD54L2	—	adipokinetic hormone receptor activity acetyl-CoA binding adiponectin binding
DE-2.43 DE-2	10	MAP3K7 SPOP GNAI1 MARCHF5 USP33	—	D2 dopamine receptor binding linear polyubiquitin binding G protein-coupled serotonin receptor binding
DE-2.44 DE-2	10	AGK MBTPS1 YTHDC2 GCFC2 SHLD2	—	ceramide kinase activity acylglycerol kinase activity
DE-2.45 DE-2	10	ATP7B DNAJC5 POM121 ZC3H7B BLTP3A	—	—
DE-2.46 DE-2	10	THBS4 ATP8B1 CLYBL ENSG00000251654 ENSG00000286980	—	phosphatidylcholine flippase activity malate synthase activity oxo-acid-lyase activity
DE-2.47 DE-2	10	SPTLC2 CHST15 VPS45 FAM83B DZIP1L	—	serine C-palmitoyltransferase activity N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity 3'-phosphoadenosine 5'-phosphosulfate binding
DE-3.1 DE-3	38	ABL1 ADAM10 WRN XPO1 PKD2	—	—
DE-3.2 DE-3	34	NF1 MT-ND5 ANK2 ELMO1 DOCK1	↑SOX17 ↑FOXH1 ↑FOXA2	GTPase regulator activity nucleoside-triphosphatase regulator activity phagocytosis, engulfment
DE-3.3 DE-3	28	PRKN ALCAM FUT8 ACYP2 ZBTB20	↑SMAD5 ↑SOX11 ↓ARID1A	—
DE-3.4 DE-3	28	MSH3 MTAP AHI1 FANCL NSD3	↑SOX11 ↑ZNF532 ↑SOX4	—
DE-3.5 DE-3	27	SNCA NTF3 GRK5 GRHL2 TRPM6	—	calcium-activated potassium channel activity calcium-activated cation channel activity monoatomic ion-gated channel activity
DE-3.6 DE-3	27	HDAC4 TRPM7 DLG1 PPP3CA NFIB	↓SMAD3 ↓ARID1A ↑SMAD5	plasma membrane bounded cell projection neuron projection chromatin
DE-3.7 DE-3	26	TNC GPC3 ADGRL3 PRDM5 ARHGAP26	↓ARID1A ↑SMAD5 ↓MIXL1	chloride-activated potassium channel activity succinate-hydroxymethylglutarate CoA-transferase activity intracellular sodium-activated potassium channel activity
DE-3.8 DE-3	26	PAK1 CNNM2 ARFGEF2 SCAI TRAK1	↓ARID1A ↑DR1 ↑HES1	GABA receptor binding
DE-3.9 DE-3	26	TGFBR1 ITGA5 KDM1A NOTCH2 ITGA6	↓ARID1A ↑SMAD5 ↑SOX4	cell surface receptor complex plasma membrane
DE-3.10 DE-3	26	PDGFRA SEMA4D SDC2 SLC12A2 REV1	↑DR1 ↓ARID1A ↑HNF1B	GABA receptor binding intracellular membrane-bounded organelle
DE-3.11 DE-3	25	YAP1 PTK2 MAPK8 ARID1B PUM1	—	chromatin immune system process positive regulation of immune system process
DE-3.12 DE-3	24	HDAC8 ST6GAL1 CASK ASAP1 KALRN	—	GTPase regulator activity nucleoside-triphosphatase regulator activity
DE-3.13 DE-3	22	NCOA2 PBX1 MSI2 KMT2C CLASP1	—	MLL3/4 complex
DE-3.14 DE-3	21	NCOA1 CBLB WWP1 NEO1 MEIS2	—	excitatory synapse glutamate receptor binding 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
DE-3.15 DE-3	19	FHIT TIAM1 SMYD3 SOX5 RAD51B	↑ZNF532 ↑SOX11 ↓CNBP	—
DE-3.16 DE-3	17	GATA3 TET1 SORL1 COL18A1 GAD1	↑SETDB1 ↑KLF8	extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength collagen trimer
DE-3.17 DE-3	17	NSD1 SND1 BIRC6 GRB10 KANK1	—	—
DE-3.18 DE-3	17	GATA4 COL4A1 JAZF1 COL4A2 PDE10A	↓ARID1A ↓SMAD3 ↑SOX4	collagen type IV trimer network-forming collagen trimer chicken-wire-like collagen network
DE-3.19 DE-3	17	DPP4 HNF1B MTSS1 PITX1 RGS5	↓CTBP1	—
DE-3.20 DE-3	16	CAMTA1 WIPF1 ADCY1 CLEC2D RTN1	—	L-fuconate dehydratase activity G protein-coupled UDP receptor activity G protein-coupled purinergic nucleotide receptor activity
DE-3.21 DE-3	16	XRCC4 CLCN5 CENPC KIAA0586 DDX10	—	—
DE-3.22 DE-3	15	FGFR1 FN1 PROS1 VCAN FOXP2	↓SMAD3 ↑DR1	extracellular matrix external encapsulating structure cell motility
DE-3.23 DE-3	15	ANTXR1 MAP2K5 PIBF1 AP3B1 APLF	↑SOX17 ↑FOXH1 ↑SMAD5	tRNA (guanine(10)-N2)-methyltransferase activity 3-hydroxyisobutyryl-CoA hydrolase activity interleukin-4 receptor binding
DE-3.24 DE-3	15	BRAF SOS1 TNKS EHMT1 COP1	—	histone H3K9 methyltransferase activity RNA metabolic process regulation of macromolecule metabolic process
DE-3.25 DE-3	15	BCL11A RBPJ AGO1 PDGFC WNK2	↓ARID1A ↓SMAD3 ↑HES1	regulation of dendrite development
DE-3.26 DE-3	15	ERCC8 PTPRA NEK1 RHBDD1 MYCBP2	—	—
DE-3.27 DE-3	14	RELN ITPR1 LINC00511 PCSK2 ARB2A	↑FOXH1 ↑SMAD4 ↑SOX17	extracellular matrix structural constituent glycine N-acyltransferase activity myosin II head/neck binding
DE-3.28 DE-3	14	MCU THADA RAP1GDS1 TLK1 CDC42BPA	—	negative regulation of endoplasmic reticulum calcium ion concentration positive regulation of mitochondrial calcium ion concentration intracellular calcium ion homeostasis
DE-3.29 DE-3	14	ATR ATF6 TRIM44 MPDZ FBXL4	—	—
DE-3.30 DE-3	13	MDM4 POT1 DCAF1 ZDHHC17 TTI1	—	G-rich single-stranded DNA binding xylosyl alpha-1,3-xylosyltransferase activity histone H2AT120 kinase activity
DE-3.31 DE-3	12	ROR1 LAMA1 FNDC3B MCC ADAMTS12	—	—
DE-3.32 DE-3	12	PTPRJ ATG10 HECW2 TBCK LDLRAD3	↑SMAD5 ↑DR1 ↓ARID1A	Atg12 transferase activity Atg12 conjugating enzyme activity
DE-3.33 DE-3	12	APP CUX1 PTPRG MAGI1 KLF12	↑SOX17 ↑SMAD5 ↑DR1	dendrite neuron spine dendritic spine
DE-3.34 DE-3	12	CLIC4 KPNA1 ZMYND11 TRIM71 SCAF4	↑DR1 ↓MIXL1 ↓SMAD3	—
DE-3.35 DE-3	12	E2F3 SMC5 MYO3A PKP4 MAST2	↑SMAD5 ↑FOXH1 ↑SOX17	glycerol-3-phosphate dehydrogenase (quinone) activity adenyl nucleotide binding plus-end directed microfilament motor activity
DE-3.36 DE-3	11	FOXP1 COL4A5 ADGRV1 FGF13 COL4A6	—	network-forming collagen trimer chicken-wire-like collagen network collagenous component of basement membrane
DE-3.37 DE-3	11	PTEN PIK3R1 KDM5B CDK19 BPTF	↑SOX11	histone demethylase activity protein demethylase activity histone H3 demethylase activity
DE-3.38 DE-3	11	KITLG LPAR1 ARL13B OVOL2 ARHGAP29	—	animal organ development 1-acylglycerophosphoethanolamine O-acyltransferase activity lysophosphatidic acid receptor activity
DE-3.39 DE-3	11	PLD1 SLC39A8 GALC MXI1 CCBE1	—	detoxification of cadmium ion stress response to cadmium ion plasma membrane selenite transport
DE-3.40 DE-3	11	TNFRSF19 MARCHF1 STK32A GPR173 PRR5L	—	gonadotropin-releasing hormone receptor activity tumor necrosis factor receptor activity death receptor activity
DE-3.41 DE-3	11	MLXIPL HHIP CPS1 EYS PDE11A	—	carbohydrate response element binding carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity carbamoyl-phosphate synthase (ammonia) activity
DE-3.42 DE-3	11	NUMA1 FANCM PCNT CEP43 MTBP	↑SOX11 ↓SMAD3 ↓ARID1A	regulation of mitotic spindle elongation regulation of spindle elongation protein localization to cytoskeleton
DE-3.43 DE-3	10	PRKCA CDKAL1 LTBP1 DGKH PDE8A	↓SMARCC1 ↓SMAD3 ↑DR1	calcium,diacylglycerol-dependent serine/threonine kinase activity histone H3T6 kinase activity microfibril binding
DE-3.44 DE-3	10	BCR TNFRSF11A SEPTIN9 XYLT1 WLS	↓ARID1A ↑SOX11	regulation of Wnt protein secretion positive regulation of heat generation circadian temperature homeostasis
DE-3.45 DE-3	10	KCNQ1OT1 NUMB CTNNA3 BTBD9 FBXL17	↑HNF1B	fascia adherens
DE-3.46 DE-3	10	PTPN13 SETBP1 UTRN MAPK10 TLN2	—	actin binding integrin binding
DE-3.47 DE-3	10	BACH1 MAPKAP1 NBAS ZFYVE9 EVI5	—	—
DE-3.48 DE-3	10	SP3 EMSY KIF2A CHD1 PPP3R1	—	pericentric heterochromatin chromatin chromosome, centromeric region
DE-3.49 DE-3	10	PBRM1 FAT1 ARSB SP4 PAXIP1	—	—
DE-3.50 DE-3	10	F2R TMPRSS2 SOX11 ATP1A1 KIF21A	—	axonal growth cone site of polarized growth synaptic membrane
DE-4.1 DE-4	67	CXCR4 IDH1 HSPB1 CDC42 PKM	—	anatomical structure development anatomical structure morphogenesis multicellular organismal process
DE-4.2 DE-4	57	FOXO3 LMNA WWTR1 MAP2K1 CTNND1	↓FOXH1 ↓SOX17 ↓TAF10	—
DE-4.3 DE-4	48	IGF1R APC TCF7L2 CDH2 MYH9	↓SMARCC1 ↓CNBP	gamma-catenin binding extrinsic component of plasma membrane extrinsic component of membrane
DE-4.4 DE-4	41	SP1 PLAUR ETS1 MSH6 NEDD4	↓SOX11 ↓SMARCC1 ↑ZNF431	sialyltransferase activity
DE-4.5 DE-4	34	NPPB CCN2 NFKBIA WFDC2 EIF4EBP1	↓SMAD5	actin cytoskeleton actin filament organization actin filament-based process
DE-4.6 DE-4	28	PNPLA3 STAT4 EDNRA JUP ST3GAL5	↓MIXL1 ↑DR1 ↓TIGD1	—
DE-4.7 DE-4	23	CFLAR FZD7 PLAGL1 C1GALT1 GRPR	—	beta-1,3-galactosyltransferase activity UDP-galactosyltransferase activity galactosyltransferase activity
DE-4.8 DE-4	23	GAS5 CDKN1C MAP1LC3A BBC3 TSPO	↑FOXH1 ↑GATA4	mitochondrial outer membrane outer membrane organelle outer membrane
DE-4.9 DE-4	22	ERBB4 NTN1 NRP2 CNTNAP2 PARD3	—	axon synaptic membrane neuron projection
DE-4.10 DE-4	22	CHFR PLAG1 BCL11B CAST CPEB4	—	terminal bouton axon terminus neuron projection terminus
DE-4.11 DE-4	21	RIGI RARB PLCE1 PRKCQ S1PR3	—	molecular transducer activity signaling receptor activity
DE-4.12 DE-4	19	JAK2 MGMT SPINK5 PDGFD CRPPA	↓SOX11 ↓SMAD5 ↓SOX4	interleukin-12 receptor binding histone H3Y41 kinase activity D-ribitol-5-phosphate cytidylyltransferase activity
DE-4.13 DE-4	18	SMAD3 ANGPT2 SYNE1 PALLD SERINC5	—	external encapsulating structure extracellular matrix basement membrane
DE-4.14 DE-4	18	STAT5B AXIN2 MYO5B SGPL1 WNK3	↓MIXL1 ↓SNAI1 ↓FOXH1	—
DE-4.15 DE-4	17	TJP1 ATP2A2 MERTK WNK1 SPTAN1	↑DNAJC19 ↓ZNF628 ↓CTBP1	—
DE-4.16 DE-4	16	IQGAP1 ARRB1 ALDH3A2 FLVCR1 BASP1	↓SMARCC1 ↑ZNF431	glomerular epithelium development glomerular epithelial cell differentiation negative adaptation of signaling pathway
DE-4.17 DE-4	16	CAPN1 SNHG16 GIPC1 PLIN3 FLII	—	—
DE-4.18 DE-4	15	MSH2 ATXN1 SGMS1 DAB1 SPOCK1	↑DNAJC19 ↓SMARCC1 ↓DNMT1	main axon neuromuscular junction axon
DE-4.19 DE-4	15	CCN1 PRKCI MAP3K8 ACTN1 NECTIN2	↓SOX11	cell-cell junction
DE-4.20 DE-4	15	RALBP1 HGS TNIP2 MKNK2 CHMP1A	—	multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway
DE-4.21 DE-4	14	ACKR3 MECOM GATA6 SLC1A1 OTX2	—	glutamate:sodium symporter activity D-aspartate transmembrane transporter activity plus-end directed microfilament motor activity
DE-4.22 DE-4	13	ABCA1 OGA AMBRA1 SPRED2 CHD2	↓FOXH1 ↑ARID1A ↓SOX11	[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity hydrolase activity, hydrolyzing O-glycosyl compounds beta-N-acetylglucosaminidase activity
DE-4.23 DE-4	13	CCL2 FGF8 CCNG1 TRIP10 FZD8	↓SOX11	type 1 fibroblast growth factor receptor binding CCR chemokine receptor binding type 2 fibroblast growth factor receptor binding
DE-4.24 DE-4	13	HSPG2 PKP2 LAMB1 CACNB2 MTHFD1L	↓SOX11 ↓SOX4	actin-mediated cell contraction cardiac conduction membrane depolarization during AV node cell action potential
DE-4.25 DE-4	12	SRF PRKAG2 DAPK3 FHOD1 FBLIM1	—	actomyosin contractile actin filament bundle stress fiber
DE-4.26 DE-4	11	PIK3CB VCL EDA FLNB AKAP13	—	cell periphery plasma membrane actin cytoskeleton
DE-4.27 DE-4	11	FERMT2 FRZB DIO3 STK26 RRBP1	↑ARID1A ↓SMAD5 ↓SOX17	cervix development oviduct development lateral motor column neuron migration
DE-4.28 DE-4	11	PAX6 SLC34A2 MTUS1 SLC26A2 LRAT	—	phosphatidylcholine-retinol O-acyltransferase activity oxalate transmembrane transporter activity O-palmitoyltransferase activity
DE-4.29 DE-4	11	SATB1 KDM6B BTG2 TERF2IP TP53INP1	—	—
DE-4.30 DE-4	10	HMGA2 ITGB5 MYOCD TNFRSF21 COLEC12	—	glycoprotein endo-alpha-1,2-mannosidase activity MH1 domain binding MH2 domain binding
DE-4.31 DE-4	10	KLF8 RBM20 MAK ZNF462 PPFIBP1	—	—
DE-4.32 DE-4	10	PRKCZ TNK2 SH3KBP1 PPP3CC ERGIC1	↓SMAD5 ↑SNAI1 ↓SIRT6	—
DE-5.1 DE-5	30	EPOR DKK3 NDRG2 DNAAF4 HPN	—	—
DE-5.2 DE-5	29	CRMP1 BANP FIG4 KREMEN1 ARHGAP18	—	—
DE-5.3 DE-5	24	VHL DNMT3A RXRA TERF2 TBX1	↑PREB	lncRNA binding tooth mineralization enamel mineralization
DE-5.4 DE-5	23	BCL2L1 EFNB2 WWC1 ADAMTS1 PNPT1	↑PSMA1 ↑MYNN	—
DE-5.5 DE-5	23	STAT6 BBS1 SLC35A1 TOM1L1 MSTO1	↑ZC3H3	—
DE-5.6 DE-5	21	PPARA TRPA1 LPIN1 BNIP3L ARID3A	—	response to food
DE-5.7 DE-5	18	SCN8A JAM3 GALNT3 RGS17 GNB5	—	—
DE-5.8 DE-5	18	CHUK MFN2 LONP1 SETD1A SART3	—	Cajal body small nuclear ribonucleoprotein complex spliceosomal snRNP complex
DE-5.9 DE-5	17	MTRR SOAT1 OTULIN SPSB1 MSL1	↑ZC3H3	transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding sterol O-acyltransferase activity
DE-5.10 DE-5	17	MED12 STAT2 PLEC HEXIM1 MADD	↓DNAJC2	—
DE-5.11 DE-5	17	HLA-E HADHB MAP9 TCTN1 ALDH6A1	—	plasma membrane bounded cell projection cell projection motile cilium
DE-5.12 DE-5	15	LANCL2 LTO1 SNAPC4 NOL4L RCL1	—	positive regulation of abscisic acid-activated signaling pathway response to abscisic acid cellular response to abscisic acid stimulus
DE-5.13 DE-5	14	GOLPH3 TEAD4 MAML1 PRPF4B LUC7L3	↑ZIC3	—
DE-5.14 DE-5	14	IRS2 IRF2 NFYC CCNL1 TENT4B	—	TRAMP complex
DE-5.15 DE-5	14	POLH ESRP1 CNTN1 RNF115 LNPK	—	regulation of inner ear auditory receptor cell fate specification regulation of inner ear auditory receptor cell differentiation auditory receptor cell fate specification
DE-5.16 DE-5	14	FBF1 ADAMTS7 DEAF1 PRMT7 CREBZF	—	—
DE-5.17 DE-5	14	ADGRG6 NCKIPSD TMEM38B ALG9 LRRC1	—	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity
DE-5.18 DE-5	14	BIRC2 IFNGR1 INSIG2 TMEM106B HEXA	—	—
DE-5.19 DE-5	13	SEC14L2 RNF170 FBXO16 PHYKPL TTC23	—	UDP-N-acetylgalactosamine transmembrane transporter activity vitamin E binding UDP-glucuronate transmembrane transporter activity
DE-5.20 DE-5	12	DHX9 SRPK1 EIF3A DDX6 AMD1	—	RNA binding ATP-dependent activity, acting on RNA transcription elongation factor activity
DE-5.21 DE-5	12	HSPA4 MED1 MFN1 NSUN2 PRPF8	—	spliceosomal complex ribonucleoprotein complex RNA binding
DE-5.22 DE-5	12	SNX27 E2F5 KIF3B ZNF268 UBE2R2	—	DNA-binding transcription factor activity transcription cis-regulatory region binding transcription regulator activity
DE-5.23 DE-5	12	CARD8 SS18 CDR2 ZFAND6 FEZ2	—	—
DE-5.24 DE-5	12	SENP3 LPCAT1 MLLT1 ITPK1 TNPO2	—	plasmalogen synthase activity inositol-3,4,5,6-tetrakisphosphate 1-kinase activity inositol-1,3,4-trisphosphate 6-kinase activity
DE-5.25 DE-5	11	TARDBP AGO2 DDX3X IGF2BP1 CUL1	—	RNA binding mRNA binding nucleic acid binding
DE-5.26 DE-5	11	CPSF6 TPR BCLAF1 SON CCAR1	—	RNA binding nucleic acid binding RNA processing
DE-5.27 DE-5	11	MTHFR SMARCAL1 RHOT1 RARRES1 FYCO1	—	—
DE-5.28 DE-5	11	ERN1 BCAR1 SETDB2 PDE6D SBNO2	—	methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity transferase activity, transferring one-carbon groups
DE-5.29 DE-5	11	NR1H3 SNAP23 COX15 TTC5 CKMT2	—	ribosome binding creatine kinase activity sterol response element binding
DE-5.30 DE-5	10	OPA3 TRIM13 FBXO25 SHPK SLC35F2	—	sedoheptulokinase activity
DE-5.31 DE-5	10	STX17 TRDMT1 KCTD20 TUBD1 PTGR3	—	—
DE-6.1 DE-6	55	BRCA1 EZH2 CHEK1 PRKDC CCNE1	↓RCOR2	DNA replication DNA metabolic process DNA-templated DNA replication
DE-6.2 DE-6	29	GRK2 PAK4 SOCS2 CSNK1E MAP2K7	—	negative regulation of peptide secretion negative regulation of hormone secretion peptide transport
DE-6.3 DE-6	24	PROM1 MCM2 POLE RNF168 STAG2	↑ARID1A ↑SMARCC1 ↑SOX11	site of double-strand break nuclear chromosome DNA recombination
DE-6.4 DE-6	22	INSR AIM2 DGCR8 MYO9B VAV2	—	—
DE-6.5 DE-6	21	DAXX RAD51C PARP2 FANCG CISD2	↓FOXH1 ↓SOX17	axonemal microtubule axoneme ciliary plasm
DE-6.6 DE-6	20	TYMS PCNA FEN1 RRM2 DEK	↓SMAD5 ↓SOX17 ↓GRHL2	DNA metabolic process DNA replication cell cycle DNA replication
DE-6.7 DE-6	20	MBD4 MAZ TXNDC5 ING2 PLEKHO1	↑ARID1A ↓SMAD5 ↑MIXL1	pyridoxal phosphate metabolic process vitamin B6 metabolic process protein disulfide isomerase activity
DE-6.8 DE-6	19	FANCD2 RAD18 LIG1 CDC7 KCNQ3	—	cell cycle process cell cycle positive regulation of cell cycle process
DE-6.9 DE-6	19	MLH1 ING5 SETMAR CAD SECISBP2	↓SMAD5 ↑ARID1A ↓SOX4	transferase activity, transferring one-carbon groups carboxyl- or carbamoyltransferase activity dihydroorotase activity
DE-6.10 DE-6	18	PLK4 DPYSL2 TIMELESS NET1 ERCC6L	↓SOX17 ↓FOXH1 ↑SNAI1	structural constituent of nuclear pore nuclear pore deuterosome
DE-6.11 DE-6	18	SIGMAR1 SV2A SLC5A6 HERC5 MYCBP	—	hormone activity biotin transmembrane transporter activity pantothenate transmembrane transporter activity
DE-6.12 DE-6	13	CHAMP1 PLIN2 RBM14 CENPS PUS1	—	steroid receptor RNA activator RNA binding
DE-6.13 DE-6	12	H1-2 H1-4 H2AC20 H1-5 H1-3	—	nucleosome chromatin protein-DNA complex
DE-6.14 DE-6	12	E2F1 CASP8AP2 CCNE2 CDC45 MCM6	—	cell cycle process cell cycle regulation of cell cycle process
DE-6.15 DE-6	12	MRE11 DDX11 RAD54B MOB3B CNTLN	—	DNA helicase activity ATP-dependent activity, acting on DNA helicase activity
DE-6.16 DE-6	12	SIAH1 RBM10 BICD2 PLEKHG2 SP2	—	—
DE-6.17 DE-6	12	EHMT2 PRMT6 EFTUD2 RHOT2 METTL13	—	N-methyltransferase activity protein methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity
DE-6.18 DE-6	11	MTHFD1 TRA2B RMI1 UBA2 NAA50	—	ligase activity GMP synthase (glutamine-hydrolyzing) activity GMP synthase activity
DE-6.19 DE-6	10	SH3GL2 CTDSPL FAM161A ZNF385B SFI1	—	—
DE-7.1 DE-7	94	HLA-B APOA1 ALDH2 IGFBP3 CST3	↓SOX11 ↓ZC3H3 ↓DR1	extracellular region extracellular space chylomicron
DE-7.2 DE-7	34	CNR1 SLC16A1 SLC11A2 TRIB2 PHF6	↑ARID1A ↑SMARCC1 ↓DR1	secondary active monocarboxylate transmembrane transporter activity symporter activity solute:monoatomic cation symporter activity
DE-7.3 DE-7	27	GJA1 FURIN SPRY2 HAS2 FZD4	↑ARID1A ↓FOXA2 ↓SNAI1	plasma membrane cell periphery cell-cell junction
DE-7.4 DE-7	17	CYP2R1 RNF20 GOPC AGGF1 APIP	—	amino acid metabolic process mitochondrial translation mitochondrial gene expression
DE-7.5 DE-7	15	HLA-C HDAC1 CTSL GSN ATP6AP2	↓SOX11	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds serpin family protein binding phosphoribosylaminoimidazolecarboxamide formyltransferase activity
DE-7.6 DE-7	14	ITGA7 SDC3 RAB11FIP2 NEDD1 PTPRU	—	—
DE-7.7 DE-7	12	TDP2 UFM1 SELENOF EIF2AK1 MPHOSPH8	↓SOX4 ↓SOX11	3-dehydrosphinganine reductase activity tyrosyl-RNA phosphodiesterase activity 5'-tyrosyl-DNA phosphodiesterase activity
DE-7.8 DE-7	12	MBOAT7 MLST8 CIB2 EPN1 EMC10	↑ARID1A ↓ZC3H3 ↓ILF3	photoreceptor inner segment
DE-7.9 DE-7	11	SERPING1 LTA4H BDH2 UROS OCIAD1	↓SOX11 ↑SMARCC1 ↓SETDB1	peptide metabolic process organic acid metabolic process carboxylic acid metabolic process
DE-8.1 DE-8	41	HTT OGT RNF213 PFKFB3 CDKL5	—	macroautophagy catabolic process mitophagy
DE-8.2 DE-8	24	ANKRD26 TSGA10 STX8 HHAT FGGY	—	—
DE-8.3 DE-8	22	MALAT1 NEAT1 AKT3 FAF1 SEMA5A	—	—
DE-8.4 DE-8	20	GLI2 HIP1 WNT5B USP13 GRIK3	—	cell junction postsynaptic density membrane postsynapse
DE-8.5 DE-8	18	CASC9 RBM47 USP9Y CAMKMT KIAA1217	↑DNAJC19	—
DE-8.6 DE-8	18	TET2 IFT88 DNAJC13 UBR1 COG6	—	lipid sensor activity 2-oxoglutarate-dependent dioxygenase activity carboxylic acid binding
DE-8.7 DE-8	16	CC2D2A TPT1-AS1 LINC00174 ARMC9 ASB3	—	—
DE-8.8 DE-8	15	CLOCK SIN3A MICU1 VPS13A ELOVL6	—	—
DE-8.9 DE-8	15	RPS6KA5 LNPEP EFHC1 EVC2 STRADA	—	calcium-dependent phospholipid binding histone H2AS1 kinase activity histone H3S28 kinase activity
DE-8.10 DE-8	14	C1RL NME7 PAX8-AS1 RSRP1 TTC14	—	—
DE-8.11 DE-8	13	ROBO1 MEF2A EYA1 GLCCI1 RASAL2	—	phosphatidylinositol deacylase activity chondroitin 2-sulfotransferase activity dermatan 2-sulfotransferase activity
DE-8.12 DE-8	13	TRPC1 NORAD PIK3C3 NRIP1 HMBOX1	—	positive regulation of protein lipidation positive regulation of lipoprotein metabolic process regulation of protein lipidation
DE-8.13 DE-8	12	TP53BP1 LGR5 PDE4D EPHA4 SLIT3	—	monoatomic ion channel complex plasma membrane protein complex dendritic spine
DE-8.14 DE-8	11	VWF DISC1 PCAT1 ANO2 IGSF11	—	—
DE-8.15 DE-8	11	PDCD4 JAK1 RICTOR ATP2B4 CREBRF	—	regulation of arginine catabolic process negative regulation of arginine catabolic process regulation of developmental process
DE-8.16 DE-8	10	SGIP1 FSIP2 ZNF33A ENSG00000214955 RAB33B-AS1	—	sperm end piece
DE-8.17 DE-8	10	PI4KA PXDN CELSR1 SH3PXD2B ADCY7	—	lateral sprouting involved in lung morphogenesis symbiont-mediated perturbation of host membrane endoplasmic reticulum polarization
DE-8.18 DE-8	10	SETDB1 SUFU ACAD10 MTFR1 CTPS2	—	histone H3K9 trimethyltransferase activity CTP synthase activity GLI-SUFU complex
DE-9.1 DE-9	54	ERBB2 CDH1 POU5F1 DNMT3B RYR2	↓DNAJC19 ↑ARID1A ↓MARS	system development multicellular organism development anatomical structure formation involved in morphogenesis
DE-9.2 DE-9	52	NRG1 VIM BMP4 NRP1 FSHR	↑ARID1A ↓SOX11	positive regulation of multicellular organismal process positive regulation of cell differentiation positive regulation of developmental growth
DE-9.3 DE-9	24	PTCH1 OPA1 PRKD1 PPP2R2B SLC20A2	—	ossification osteoblast differentiation membrane bending activity
DE-9.4 DE-9	16	MT-ATP6 PLCG2 MT-ND4 MT-ND2 MT-CO1	↓SOX17	respiratory chain complex proton transmembrane transporter activity oxidative phosphorylation
DE-9.5 DE-9	14	CADM1 SLIT2 ETV1 VAV3 GRIK2	↑CNBP ↓SOX17	myelin assembly detection of cold stimulus involved in thermoception negative regulation of neutrophil migration
DE-9.6 DE-9	13	FKBP5 IGFBP2 TGFBR3 EPHA7 CAMK1D	↑ARID1A ↓SOX17	cellular developmental process cell differentiation muscular septum morphogenesis
DE-9.7 DE-9	11	TGFB1 ITGB1 TNFRSF10B ADAMTS9 IGFBP4	—	molecular transducer activity signaling receptor activity cell surface
DE-9.8 DE-9	10	PRKG1 SYT1 NFIA ITPR2 BNC2	—	clathrin-sculpted glutamate transport vesicle membrane clathrin-sculpted monoamine transport vesicle membrane clathrin-sculpted glutamate transport vesicle
DE-10.1 DE-10	28	AHR TGFBR2 NPC1 GCH1 USP28	↑SMARCC1	—
DE-10.2 DE-10	27	RAB1A GFPT1 SEL1L UGDH HYOU1	↑ARID1A ↑SMARCC1 ↓SNAI1	endoplasmic reticulum endoplasmic reticulum to Golgi vesicle-mediated transport endomembrane system
DE-10.3 DE-10	24	NF2 CTTN ACTN4 GCLC CAMK2G	↑ARID1A ↑SMARCC1 ↓RFX7	intracellular vesicle cytoplasmic vesicle endosome
DE-10.4 DE-10	20	CD46 GRB2 RAB5A RAB7A CDK7	↓MARS ↑ARID1A ↓SETDB1	process utilizing autophagic mechanism autophagy macroautophagy
DE-10.5 DE-10	19	RUNX2 XIAP MFSD8 FBH1 ARHGEF18	↓DNAJC19 ↑TGIF1 ↑GATAD2A	—
DE-10.6 DE-10	18	HIF1A POLR2A STX6 UHMK1 RAB43	↑SMARCC1 ↓RFX7 ↑ARID1A	transcription cis-regulatory region binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding
DE-10.7 DE-10	14	MAPK9 SMYD2 AVEN SETD3 AAGAB	↓DR1 ↑SMARCC1 ↑ARID1A	histone modifying activity histone H3K36 methyltransferase activity protein-lysine N-methyltransferase activity
DE-10.8 DE-10	11	LIN28A F11R SKIL PRKD2 RALB	—	—
DE-10.9 DE-10	10	GABPA FIP1L1 SLC12A7 TRIT1 PIGG	—	CP2 mannose-ethanolamine phosphotransferase activity tRNA dimethylallyltransferase activity mannose-ethanolamine phosphotransferase activity
DE-10.10 DE-10	10	PTPN1 RAP1B MAPK6 RAB21 FBXL3	—	—
DE-11.1 DE-11	70	MKI67 AURKA PLK1 CDK1 TOP2A	↑FOXH1 ↑SMAD3 ↑SMAD4	mitotic nuclear division nuclear division cell cycle process
DE-11.2 DE-11	25	CHEK2 IDH2 CTCF XRCC5 SLC29A1	↑SNAI1 ↑SMAD3 ↑MIXL1	chromosome chromosomal region nuclear lumen
DE-11.3 DE-11	22	FOXM1 CIP2A WEE1 CBX5 PBK	↑SMAD4 ↑FOXH1 ↑SMAD3	mitotic cell cycle mitotic cell cycle process cell cycle
DE-11.4 DE-11	17	SRSF1 EIF4G1 NONO LIG3 MATR3	↑E2F6 ↑FOXH1	nuclear lumen nuclear protein-containing complex nucleoplasm
DE-11.5 DE-11	14	BIRC5 PTTG1 CDC20 HMMR DYNLL1	↑FOXH1 ↑E2F6 ↑SOX17	spindle microtubule cytoskeleton cytoskeleton
DE-11.6 DE-11	13	NCL HNRNPA2B1 HNRNPD MARCKS SFPQ	—	RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome
DE-11.7 DE-11	10	PTBP1 TCOF1 GORASP2 DHX33 SF1	—	sphingophospholipase activity RNA binding sphingomyelin phosphodiesterase activity
DE-12.1 DE-12	43	KIT PDPN PVR CDH3 DAB2	↑ADNP2 ↑SETDB1 ↑CHAMP1	regulation of vesicle-mediated transport vesicle-mediated transport positive regulation of clathrin-dependent endocytosis
DE-12.2 DE-12	33	CHRM3 STS PDK1 SLCO1A2 TNNT1	↑SETDB1 ↑DNMT1 ↑ZNF850	—
DE-12.3 DE-12	25	TRIM24 TUSC3 DLEU1 ATF7IP CPLANE1	—	—
DE-12.4 DE-12	13	BST2 FEZ1 COL6A2 RMST CLTB	—	negative regulation of plasmacytoid dendritic cell cytokine production negative regulation of dendritic cell cytokine production regulation of plasmacytoid dendritic cell cytokine production

Cluster	Genes	Notable Genes	Top TF Regulators	Top Enriched Terms
GC4	1049	BRCA1 MYC AR COMT BCL2	↑ARID1A ↑SMARCC1 ↑CNBP	—
GC5	1037	SIRT1 MET SOD1 FGFR1 SOX2	↑SMARCC1 ↑CNBP ↓DNAJC19	—
GC3	570	STAT3 MMP9 CDH1 MMP2 CD44	↑FOXH1 ↑SMAD4 ↑SMAD3	—
GC1	548	HIF1A ERBB2 CTNNB1 ITGB1 LDLR	—	—
GC2	587	TGFB1 MDM2 HLA-DQB1 HLA-A AGER	↑FOXH1 ↓ARID1A ↑SOX17	—
GC6	1040	AKT1 HLA-DRB1 CXCR4 IGF1R MAPK3	↓ARID1A ↓SMARCC1 ↓MIXL1	—

Module	Genes	Notable Genes	Top TF Regulators	Top Enriched Terms
DE-1	2012	APOE KRAS GSTP1 HMGB1 SOD1	↑CTBP1 ↑SOX11 ↓KLF6	ribonucleoprotein complex ribosomal subunit structural constituent of ribosome
DE-2	1440	CTNNB1 MTOR MAPK1 PIK3CA MDM2	↓CTBP1 ↑TCEB3 ↑ZC3H3	catalytic activity, acting on a protein protein serine/threonine kinase activity phosphotransferase activity, alcohol group as acceptor
DE-3	1094	APP BRAF PTEN SNCA ATM	↓ARID1A ↑SMAD5 ↑SOX11	cell periphery cell projection plasma membrane bounded cell projection
DE-4	1090	CXCR4 JAK2 CCL2 NPPB IGF1R	↓CTBP1 ↓SOX11 ↑TCEB3	cell periphery plasma membrane anatomical structure development
DE-5	1025	MTHFR NFKB1 NFE2L2 SIRT1 SOD2	↑ZC3H3	transcription cis-regulatory region binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding
DE-6	662	BRCA1 BRCA2 EZH2 ESR2 MLH1	↑ARID1A ↓SMAD5 ↓FOXH1	DNA metabolic process DNA replication DNA-templated DNA replication
DE-7	389	HLA-B APOA1 HLA-C ALDH2 IGFBP3	↑ARID1A ↓SOX11 ↓SNAI1	endoplasmic reticulum lumen endoplasmic reticulum chylomicron
DE-8	360	VWF HTT MALAT1 MTR NEAT1	—	cilium sperm flagellum motile cilium
DE-9	338	TP53 TGFB1 STAT3 ERBB2 CDH1	↑ARID1A ↓DNAJC19 ↑SMARCC1	cell periphery multicellular organismal process plasma membrane
DE-10	327	HIF1A SRC MCL1 AHR RUNX2	↑ARID1A ↑SMARCC1 ↓RFX7	vesicle-mediated transport transport endosomal transport
DE-11	267	BIRC5 MKI67 AURKA PLK1 FOXM1	↑FOXH1 ↑SMAD4 ↑SMAD3	cell cycle mitotic nuclear division mitotic cell cycle
DE-12	152	KIT LGALS1 RIPK1 PDPN BST2	↑SETDB1 ↑DNMT1 ↑ADNP2	—

Module Overview