Composition of recurrent gene modules

SignatureGenes
CycleACYP1, ANLN, ANP32B, ANP32E, APITD1, APOBEC3B, ARHGAP11A, ARHGAP11B, ARL6IP1, ARL6IP6, ASF1B, ASPM, ATAD2, ATAD5, AURKA, AURKB, BARD1, BCL2L12, BIRC5, BORA, BRCA1, BTG3, BUB1, BUB1B, C12orf75, C19orf48, C21orf58, CALM2, CALM3, CARHSP1, CASC5, CCDC34, CCNA2, CCNB1, CCNB2, CCNE1, CCNE2, CCT5, CDC20, CDC25B, CDC45, CDC6, CDCA2, CDCA3, CDCA4, CDCA5, CDCA7, CDCA8, CDK1, CDKN3, CDT1, CENPA, CENPE, CENPF, CENPH, CENPK, CENPM, CENPN, CENPU, CENPW, CEP55, CHAF1A, CHEK1, CKAP2, CKAP2L, CKAP5, CKLF, CKS1B, CKS2, CLSPN, CMC2, CNIH4, CRNDE, DBF4, DDX39A, DEK, DEPDC1, DEPDC1B, DHFR, DIAPH3, DLGAP5, DNAJC9, DNMT1, DONSON, DSN1, DTL, DTYMK, DUT, E2F1, ECT2, EZH2, FADS1, FAM111A, FAM111B, FAM64A, FAM83D, FANCA, FANCD2, FANCI, FBLN1, FBXO5, FEN1, FOXM1, GGCT, GGH, GINS2, GMNN, GPSM2, GTSE1, H1F0, H2AFV, H2AFX, H2AFZ, HAUS1, HELLS, HINT1, HIRIP3, HIST1H1D, HIST1H1E, HIST1H2BJ, HIST1H4C, HIST2H2AC, HJURP, HMG20B, HMGB1, HMGB2, HMGB3, HMGN2, HMMR, HN1, HNRNPA1, HNRNPA2B1, HPRT1, HSPD1, ILF2, IQGAP3, ITGB3BP, JPT1, KIAA0101, KIAA1524, KIF11, KIF14, KIF15, KIF18A, KIF20A, KIF20B, KIF22, KIF23, KIF2C, KIF4A, KIFC1, KNSTRN, KPNA2, LIG1, LMNB1, LMNB2, LSM4, LSM5, MAD2L1, MAPRE1, MCM10, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MELK, MIS18A, MIS18BP1, MKI67, MLF1IP, MMS22L, MND1, MNS1, MSH2, MSH6, MTHFD1, MXD3, MYBL2, MZT1, NAP1L1, NASP, NCAPD2, NCAPD3, NCAPG, NCAPG2, NDC80, NEK2, NMU, NRM, NUCB2, NUCKS1, NUDT1, NUF2, NUSAP1, OIP5, ORC6, PAQR4, PARPBP, PBK, PCLAF, PCNA, PHF19, PIF1, PKMYT1, PLK1, POC1A, POLD3, PRC1, PRIM1, PRKDC, PRR11, PSIP1, PSMC3IP, PSRC1, PTMA, PTMS, PTN, PTTG1, RACGAP1, RAD21, RAD51, RAD51AP1, RAD51C, RAN, RANBP1, RBL1, RECQL4, RFC2, RFC3, RFC4, RFC5, RMI2, RNASEH2A, RNASEH2B, RNF26, RPA2, RPA3, RRM1, RRM2, SAPCD2, SGOL1, SGOL2, SHCBP1, SIVA1, SKA2, SKA3, SLBP, SLC25A5, SLC43A3, SMC1A, SMC2, SMC4, SNRNP25, SNRPB, SNRPD1, SPAG5, SPC24, SPC25, SPDL1, STMN1, STRA13, SUN2, SYT8, TACC3, TCF19, TEX30, TFDP1, TK1, TMEM106C, TMEM97, TMPO, TNFAIP8L1, TOP2A, TPX2, TRIP13, TROAP, TTK, TUBA1B, TUBA1C, TUBB, TUBB4B, TUBB6, TUBG1, TYMS, UBE2C, UBE2S, UBE2T, UHRF1, UNG, USP1, VRK1, WDR34, WDR76, ZWILCH
StressABHD3, AC016629.8, ADAMTS1, ANKRD28, ANKRD37, ARC, AREG, ARID5B, ARL5B, ATF3, B3GNT5, BAG3, BAMBI, BBC3, BHLHE40, BIRC3, BRD2, BTG1, BTG2, C10orf10, C11orf96, C16orf98, C1orf63, C5orf45, C8orf4, CA12, CCL20, CCNL1, CCP110, CD55, CDKN1A, CDKN2AIP, CEBPB, CEBPD, CITED2, CLDN3, CLDN4, CLK1, CSRNP1, CXCL1, CXCL2, CXCL3, CXCL5, CXCL8, CYP1B1, CYR61, DAPP1, DEPP1, DNAJA1, DNAJA4, DNAJB1, DNAJB4, DSC3, DUSP1, DUSP10, DUSP14, DUSP2, DUSP5, EDN1, EFNA1, EGR1, EGR2, EGR3, EHF, EIF4A2, ELF3, EMP1, EPHA2, EREG, ERRFI1, ETS2, FADS3, FAM133B, FAM46A, FAM53C, FGFR3, FHL2, FKBP4, FOS, FOSB, FOSL1, FOSL2, FRMD4B, FUS, GADD45A, GADD45B, GADD45G, GDF15, GEM, GOLGB1, HBEGF, HES1, HEXIM1, HNRNPU-AS1, HSP90AA1, HSPA1A, HSPA1B, HSPA5, HSPA6, HSPA8, HSPB1, HSPH1, ID1, ID2, IER2, IER3, IER5, IFRD1, IL8, IRX2, ITPKC, JAG1, JUN, JUNB, JUND, KCNQ1OT1, KDM6B, KIAA1683, KLF10, KLF2, KLF4, KLF5, KLF6, LDLR, LIF, LIMA1, LINC00910, LINC00936, LMNA, MAFB, MAFF, MALAT1, MAP3K8, MCL1, METTL15, MIDN, MIR222HG, MIR24-2, MIR3064, MKNK2, MXD1, MYADM, MYC, MYLIP, NAMPT, NCOA7, NEAT1, NEDD9, NFKBIA, NFKBID, NFKBIZ, NOP58, NPAS4, NR4A1, NR4A2, NRARP, NSUN6, OVOL1, PDK4, PDLIM3, PGM2L1, PHLDA1, PHLDA2, PIM1, PIM3, PLAUR, PLK2, PLK3, PMAIP1, PNRC1, POLG2, PPP1R10, PPP1R15A, PRKCA, PRPF40A, PTGS2, PTRHD1, RAB11FIP1, RAB3IP, RALGDS, RASD1, RDH10, REL, RGS2, RHOB, RND1, RND3, RP1-313I6.12, RP11-182L21.6, RP5-821D11.7, RP6-99M1.2, RRAD, SEMA4A, SERTAD1, SFN, SIK1, SLC20A1, SLC38A2, SNHG12, SOCS1, SOCS3, SOX4, SOX9, SQSTM1, TACSTD2, TAF1D, TCF7, TCIM, TFRC, TGIF1, TIPARP, TLE4, TM4SF1, TNFAIP2, TNFAIP3, TRIB1, TSC22D1, TSC22D3, UBC, UGDH, VPS37B, WEE1, YBX3, YME1L1, YOD1, ZBTB43, ZC3H12A, ZFAND2A, ZFP36, ZFP36L1, ZFP36L2, ZNF165, ZNF430
InterferonACTN1, APOL1, APOL2, APOL3, APOL6, B2M, BST2, C19orf66, C1R, C1S, C3, C5orf56, CCL2, CCL27, CCL5, CD74, CFB, CFH, CMPK2, CX3CL1, CXCL10, CXCL11, CXCL9, DDX58, DDX60, DDX60L, DYNLT1, EIF2AK2, EPSTI1, ETV7, FXYD5, GBP1, GBP2, GBP3, GBP4, GBP5, GLUL, HAPLN3, HELZ2, HERC5, HERC6, HLA-A, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB5, HLA-E, HLA-F, HSPB8, ICAM1, IDO1, IFI16, IFI27, IFI35, IFI44, IFI44L, IFI6, IFIH1, IFIT1, IFIT2, IFIT3, IFITM1, IFITM2, IFITM3, IL32, IRF1, IRF7, ISG15, ISG20, KLHDC7B, LAMP3, LAP3, LGALS3BP, LGALS9, LY6E, MDK, MSRB1, MX1, MX2, NNMT, NT5C3A, NUB1, OAS1, OAS2, OAS3, OASL, PARP14, PARP9, PDZK1IP1, PLSCR1, PSMB10, PSMB8, PSMB9, PSME1, PSME2, RARRES3, RNF213, RSAD2, RTP4, SAA1, SAMD9, SAMD9L, SAMHD1, SERPING1, SERPINH1, SLFN5, SOD2, SP100, SP110, SPP1, SQRDL, STAT1, TAP1, TAP2.1, TAPBP, TGM2, TNFSF10, TNFSF13B, TRIM22, TYMP, UBD, UBE2L6, USP18, VCAM1, WARS, XAF1, ZC3HAV1, ZNFX1
HypoxiaADM, AHNAK, ALDOA, ANGPTL4, BLNK, BNIP3, BNIP3L, C4orf3, CA9, CASP14, DDIT4, DHRS3, EGLN3, ENO2, EPAS1, ERO1L, FAM162A, FUT11, HILPDA, HK2, IGFBP3, LDHA, LINC01133, MGP, NDRG1, NDUFA4L2, NRN1, P4HA1, PDK1, PFKFB3, PFKP, PGF, PGK1, PLIN2, PLOD2, PTHLH, RGCC, SLC16A1, SLC16A3, SLC2A1, SLC2A3, SLC6A8, SNCG, SPAG4, TMEM91, VEGFA
OxphosATOX1, ATP5H, C14orf2, COX14, MYEOV2, NDUFA1, NDUFA12, NDUFA3, NDUFB3, NDUFS6, NME1, PET100, POLR2I, POLR2L, RBX1, ROMO1, SCAND1, SEPW1, SLIRP, TIMM8B, TXNDC17, UQCR10, USMG5, UXT
MetalFKBP5, HEY1, HTRA1, MT1F, MT1G, MT1H, MT1M, PMP2, TPST1
MesenchymalAQP1, BGN, CALD1, CCDC80, COL1A1, COL1A2, COL3A1, COL5A2, COL6A1, COL6A3, CPE, FN1, GJA1, GNG11, NPC2, NRP2, SDC2, SPARC
pEMTACTB, ACTG1, ADIRF, AKAP12, AKR1C1, ANXA1, ANXA2, ANXA3, ANXA5, ARL4C, ARPC1B, BCAM, BPGM, C19orf33, CAPN2, CD151, CD24, CD44, CD59, CD68, CD9, CD99, CDA, CDKN2A, CFL1, CHI3L1, CLIC1, COTL1, CRIP1, CSTB, CTGF, CTSB, DKK1, ECM1, EIF4EBP1, EIF5A, EMP3, ENO1, F3, FLNA, FLNB, FSTL3, FTL, G0S2, G6PD, GAPDH, GJB6, GLO1, GPI, GPX1, HMGA1, IGFBP2, IGFBP6, IGFBP7, INHBA, ITGA6, ITGB1, ITGB6, ITGB8, ITM2B, KLK6, KRT17, KRT18, KRT19, KRT7, KRT8, KYNU, LAMA3, LAMB3, LAMC2, LGALS1, LGALS3, LINC00152, MGST1, MIF, MMP1, MMP3, MT1E, MT2A, MYH9, MYL12B, MYL6, MYO1B, OCIAD2, ODC1, PDLIM4, PDLIM7, PDPN, PFN1, PFN2, PGAM1, PKM, PLA2G16, PLAU, PLEK2, PLP2, PMEPA1, PODXL, PRKCDBP, PRSS23, PTRF, RBP1, RHOC, RHOD, S100A10, S100A11, S100A13, S100A16, S100A2, S100A6, SERINC2, SERPINE1, SERPINE2, SH3BGRL3, SLC25A6, SLC38A5, SMS, SPINK6, STEAP4, STOM, SULT1E1, TAGLN, TAGLN2, TGFBI, THBS1, TIMP1, TIMP3, TMSB10, TMSB4X, TNC, TNFRSF12A, TNFRSF21, TNFRSF6B, TPM1, TPM2, TPM4, TRIM29, TSHZ2, TXN, UACA, VIM, WDR1, YBX1, ZBED2
AlveolarAGER, CAPN8, CAV1, CAV2, CLIC5, CST6, CYP4B1, EMP2, FXYD3, LMO7, MYL12A, MYL9, RARRES2, SCEL, TNNC1, TRAM1
BasalALDH3A1, ASPN, ASS1, ATP1B3, COL17A1, COL18A1, CXCL14, DCN, DST, FBXO32, FTH1, GABRP, GPNMB, HOPX, ITGB4, JMJD1C, KRT14, KRT15, KRT5, NAV2, NDRG2, PDLIM1, SFRP1, SLITRK6, THBS2, TP53AIP1, TPT1, TXNIP, UBA52, UQCRH, VCAN, VTCN1, ZFAND5
SquamousAKR1B10, AQP3, C10orf99, CA2, CALML3, CALML5, CD14, CDH1, CLDN7, CRABP2, DEFB1, DMKN, DSC1, DSC2, DSG1, DSP, FABP5, FGFBP1, GJB2, GRHL3, IGFL1, IVL, KLC3, KLK10, KLK11, KRT1, KRT10, KRT16, KRT2, KRT6A, KRT6B, KRT6C, KRTDAP, LGALS7B, LY6D, LYPD3, MALL, P2RY2, PKP1, PLA2G4E, PRSS3, PVRL4, RAB25, RHOV, S100A14, S100A7, S100A8, S100A9, SAA2, SBSN, SERPINB13, SERPINB3, SERPINB4, SLPI, SPINK5, SPRR1B, SPRR2A, SPRR2D, SULT2B1, THBD, TMEM45A, TMPRSS4, TUBB2A, ZNF750
GlandularAGR2, AQP5, BCAT1, C15orf48, CD47, CEACAM5, CEACAM6, CLDN10, CLDN18, CLU, CP, CREB3L1, CST2, CST4, CTSS, CYP3A5, DHRS9, DMBT1, FMOD, GPX2, IGFBP5, IL1R2, KIAA1324, KRT23, LCN2, LGALS4, LTF, LYZ, MAL2, MIA, MMP7, MUC1, MUC16, MUC5AC, MUC5B, NAPSA, NQO1, OLFM4, ONECUT2, PGC, PHGR1, PIGR, PLA2G2A, PLAC8, PLAT, PPP1R1B, PSCA, PTGES, REG1A, REG4, RNASE1, S100A4, S100P, SCD, SCGB1D2, SERPINA1, SERPINB1, SFTPD, SPINK1, SPINT2, SQLE, TCN1, TFF1, TFF2, TFF3, TM4SF4, TMEM176A, TMEM176B, TSPAN8, WFDC2
CiliatedAC007906.2, AGR3, ARMC3, C1orf194, C20orf85, C5orf49, C9orf116, C9orf24, CALM1, CAPS, CAPSL, CCDC146, CCDC170, CETN2, CFAP126, CFAP157, CFAP43, CSPP1, CTXN1, DNAAF1, DNAH12, DNALI1, DYNLL1, EFHC1, FAM183A, FAM229B, FOXJ1, LRRC23, LRRIQ1, MORN2, MS4A8, PIFO, PPIL6, PSENEN, ROPN1L, RSPH1, SPATA18, TPPP3, UBXN10
ACAGT, ALDOC, APOE, AQP4, BBOX1, CASQ1, CPVL, CRYAB, CSRP1, CYSTM1, DKK3, DOK5, EEPD1, EFEMP1, EZR, GABRB1, GATSL3, GFAP, GRAMD3, ID3, ID4, LAMP5, LCAT, LPL, MLC1, MT1X, NTRK2, OLFM2, PLTP, PMP22, PRLHR, SPARCL1, SPOCK1, TBC1D10A, VAMP5
OPCASCL1, MAP3K1, MMP2, OLIG1, OLIG2, SEZ6L, SOX8, WSCD1
NPCARL4D, CAMK2N1, CCNG2, CELF4, CELF5, DAAM1, DCX, DLX1, DLX2, DLX5, DLX6, DLX6-AS1, GPC2, KIF5C, KLHDC8A, KLHL35, LBH, MEIS2, MIAT, NREP, NSG1, PAK3, RAB3A, RBFOX2, SOX11, STMN2, STMN4, SYT1, TAGLN3, TMSB15A

Transcription factors identified using SCENIC

SignatureGenes
CycleEZH2, POLE3, TFDP1
StressATF3, CEBPB, FOSB, JUN, JUNB
InterferonBCL11A, CD59, ETV6, IRF1, IRF2, IRF3, IRF7, IRF9, RELA, STAT1, STAT2, STAT3
HypoxiaHIF1A, JDP2, NFATC1
OxphosCD59, EGR4, ERF, FOS, HDAC2, MAZ, MEIS1, NFYB, POLE4, RCOR1, RXRA, SIX5, SMARCC2, SMC3, THAP11, YY1, ZBTB7B, ZNF345, ZNF749
MetalFOXP1, GTF2B, HDAC1, HIF1A, HMGB2, ID1, JUNB, NFKB1, NR1H2, OVOL2, POLR3G, RFX5, SP3, STAT1, ZNF189, ZNF319, ZNF429, ZNF716
cEMTFOXP1, FOXP4, MTA3, NFKB1, SRF, TCF7L2, ZNF189
pEMTFOSL1, NFE2L2
AlveolarCREB3, ZNF74
BasalGRHL1
SquamousCEBPA, CEBPB, CEBPD, FOS, GATA3, GRHL1, GRHL2, JUN, JUNB, JUND, KLF4, MAF, MAFB, SMARCA4, STAT3, TFCP2, XBP1, ZNF770
GlandularBCL3, CREB3L1, ELF3, FOS, JUN, NFKB1, POLD2, STAT3, TFF3, THRB, XBP1
CiliatedFOXA2, HNF1B, POU2F1, RFX2, RFX3, RFXANK, SOX4
ACKLF9, ZNF148
OPCATF4, BCL6, CREB1, CREB3L2, CRX, DBP, E2F3, ETS1, ETV3, FOXJ3, FOXN3, FOXO3, FOXP1, FOXP2, GTF2F1, HSF4, IRF2, KLF8, MEF2C, MYC, NFE2L1, NR2C1, ONECUT2, PKNOX2, REST, SOX11, SOX4, SOX5, SOX6, SOX8, SP3, SREBF2, TBP, TCF12, ZMIZ1, ZNF91
NPCATF6B, DLX1, DLX5, HDAC2, HOXB3, HOXC9, KLF10, KLF7, MEIS2, OLIG2, SOX11, SOX2, SOX4, VEZF1

Differentially expressed genes between M1 and M2 macrophages

SignatureGenes
M1ACTN1, ALOX5AP, ANP32E, ANXA5, B3GNT5, BAG3, BCL2A1, C15orf48, C1QBP, CCL20, CCL3L1, CCL4L2, CCL7, CD9, CLEC5A, CMPK2, DNAJB1, DNTTIP2, DUSP2, EGLN1, EIF1AX, EIF2AK2, FAM129B, G0S2, G3BP2, GBP1, GPR183, HK2, HMGN1, HSPA1B, HSPH1, IER3, IER5, IFI44L, IFI6, IFIT1, IFIT2, IFIT3, IFITM3, IL1B, IL1RN, ISG15, KLF6, LGALS1, LPCAT2, LSP1, LY6E, MAFF, MANF, MT1H, MT1M, MT1X, MX1, NDRG1, NFKBIZ, NLRP3, NT5C3A, OAS2, OLR1, PLAU, PNP, PPP1R15A, PRDM1, RASGEF1B, RGCC, RGS1, RGS10, RIPK2, RSAD2, SAMD9L, SEC61G, SFPQ, SLC2A1, SLFN5, SMC1A, SPP1, TGFBR1, TNF, TNFAIP3, XAF1, XPO6
M2ABCA1, ABHD5, ACP5, APOE, ARL4C, ASAH1, BRD4, C1QA, C1QB, C1QC, C2, C5AR1, CD14, CD163, CDC42BPB, CFD, COLEC12, CR1, CTSL, CUX1, CXCL16, EVI2A, FCGRT, FCHSD2, FOLR2, FOXP1, FTL, FYB1, GALC, GMPR2, HLA-DMA, HLA-DMB, HLA-DPB1, HLA-DRA, HTT, IL2RA, LIPA, LYZ, MAN1C1, MARCO, ME1, MOSPD2, MS4A4A, MS4A6A, MS4A7, MTSS1, OLFML2B, PDK4, PILRA, PLD3, PLTP, POU2F2, PXN, RGS2, SDC3, SELENOP, SLC12A7, SLC9A9, SNX5, SOCS3, THEMIS2, TIMP1, TMEM176B, TMEM37, TNFRSF1B, TSC22D3, TXNIP, VMO1, VNN2, VSIG4, ZBTB20, ZFHX3, ZFP36L2, ZNF331

Ref1

  1. Barkley, D., Moncada, R., Pour, M. et al. Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment. Nat Genet 54, 1192–1201 (2022). https://doi.org/10.1038/s41588-022-01141-9 ↩︎