Gene Score Library
Recommendation: 【Bioinformatics】 Bioinformatics Index
1. Overview
2. BP
3. CC
4. MF
5. Others
a. Gene Library
1. Overview
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2. BP(biological process)
○ Fibrosis marker: COL1A1, COL3A1, COL5A1, SPP1, FN1, POSTN, FGF1, PDGFB, CTGF, FGF7, IL34, CDC42, CXCL12 (SDF1), TGFBR1, TGFBR2, CCL3, CCL4, COL5A2, ADIPOQ
○ Corona virus invasion pathway: ACE2, TMPRSS2, PCK5, PCSK7, CTSL, CTSB, NRP1
○ Hypoxia related score: DCN, DDIT4, PRKCA, NDRG1
○ Genes that express high in the G1/S phase during the cell cycle
○ CEP57, CDCA7L (ref)
○ TYMS, ATAD2, RRM2, KIAA0101, TK1, PCNA, DNMT1, UBE2T, DUT, DHFR, TUBB, CENPM, RAD51AP1, ZWINT, RNASEH2A, TMEM106C, HMGB2, TUBA1B, HIST1H4C, HELLS, CLSPN, FEN1, NUSAP1, STRA13, CDK1, RFC4, RRM1, DNAJC9, WDR34, STMN1, USP1, CENPU, ASF1B, GMNN, SLBP, FAM111B, CENPK, PHGDH, PSMC3IP, CHAF1A, RFC2, WDR76, CDK4, RPA2, GGCT, MCM7, CDC6, MCM3, EZH2, PSIP1, SPC25, NASP, TMPO, TUBG1, TEX30, PKMYT1, SIVA1, MTHFD2 (ref)
○ Genes that express high in the S phase during the cell cycle: ABHD10, CCDC14, CDKN2AIP, NT5DC1, SVIP, PTAR1 (ref)
○ Genes that express high in the G2 phase during the cell cycle: ANKRD36C, YEATS4, DCTPP1 (ref)
○ Genes that express high in the G2/M phase during the cell cycle
○ SMC4, TMPO, LMNB1, HINT3 (ref)
○ CENPF, CCNB1, TOP2A, TPX2, CDC20, NUSAP1, BIRC5, CDKN3, MKI67, PRC1, CCNB2, HMGB2, PTTG1, ARL6IP1, KPNA2, UBE2S, CKS2, UBE2C, TUBB4B, ANP32E, AURKB, CDK1, MAD2L1, KIF20B, TACC3, KNSTRN, CDCA3, CKS1B, SMC4, RACGAP1, TUBA1C, HMGB3, UBE2T, ASPM, SGOL2, PLK1, GTSE1, CEP55, ECT2, CCNA2, NUF2, CKAP2, TROAP, DEPDC1, AURKA, TUBA1B, PBK, CDC25B, CENPW, CALM2, GPSM2, BUB3, CENPA, SKA2, NEK2, HN1, HMMR, KIF23, KIFC1, TUBB, CDCA8, KIF2C, HMGN2, FAM83D, DLGAP5, CENPE, STMN1, TMPO, DBF4, EMC9, DTYMK, FAM64A, PTMS, NDC80, NCAPD2, FOXM1, H2AFX, CKAP5, SGOL1, RAD21, MZT1, SUN2 (ref)
○ Genes that express high in the M phase during the cell cycle: HMG20B, HMGB3, HPS4 (ref)
○ Genes that express high in the G0 phase during the cell cycle: CDKN1A, CDKN1B, CDKN1C (ref)
○ Cell cycle related score: CDC20, CCNB1, CENPF, PTTG1
○ Regulation of cell growth: AREG, EGR1
○ Vascular remodeling: VEGFB, VEGFC, ANGPTL4
○ Type 1 immunity: CCL3, CXCL9, CXCL10, CXCL11, IL18
○ Type 2 immunity: CCL11, CCL13, CD5L, IL4, IL5, IL13, IL24
○ Immune activation: CD40LG, CD48, CD80, CD86
○ Metastasis: PLAU, PLAUR, RELB, AREG
○ Immune checkpoint genes: HAVCR2, CD47, LGALS9, CD276, LAG3, PDCD1, BTLA, CD274 (PD-L1), PDCD1LG2 (PD-L2), VSIR, MIF, SIGLEC10, CTLA4, TIGIT, CD96, TNFRSF1B
○ Proliferation genes: MKI67, MCM2, PCNA, STMN1, Mki67, Mpp1
○ Immunosuppression: APOE, GPNMB
○ E2F targets: ATAD2, MCM2, BIRC5
○ Neuron differentiation: STMN2, STMN4, NTUBB3
○ Antigen presentation: CD74, HLA-DRB1, HLA-DQA2, HLA-C, HLA-DRB5
○ antigen processing: LY75, TAP1
○ migratory marker: CCR7, CCL19
○ keratinization: SPRR2D, SPRR2E, SPRR2A, CRCT1, CNFN
○ cell apoptosis: FOXO3, MCL1
○ malignancy score: KRT18, IRX2, NAPSA, SPINK13, KRT7, CAPN8, GPRC5A
○ immune response: STAT4, MYB
3. CC(cellular component)
○ Complement activation: C1QA, C1QB, C1QC, CFD, C7
○ Immunoglobulin: IGKC, IGKV4-1, IGHA1, IGHG2, IGLV9-49, IGHV1-46
○ Extracellular matrix: FBLN, COL1A2, COL3A1, BGN, COL1A1, COL1A2, SPP1, FN1, TIMP1, COL6A2, LYPD3, SLPI, MT2A, NIME2, IFITM3, DCN, TNC
○ Tissue resident marker: NR4A1, NR4A2, NLRP3
○ T cell receptor(TCR): TRAC, TRBC, TRDC, Cd3e, Cd4, Cd8a
○ MHC molecules: HLA-DRA, HLA-DPA1, HLA-C, HLA-DRB5, HLA-DQA2
○ MHC Class II: H2-ab1, H2-aa, H2-eb1
○ Melanin production and packaging: Tyrp1, Dct, Pmel, Mlana
○ Glutamate receptors: GRIK1, GRIK3, GRIK5
○ Voltage-gated potassium channel: KCND3, KCNK1, KCNMA1, KCNQ2, KCNT1
○ Voltage-gated calcium channel: CACNA1A, CACNA1C, CACNA2D1
○ Microtubule organization/trafficking: DYNC2LI1, KIF3A, CFAPs, IFTs, MCTL1
○ Synaptic vesicle transport and release: KIF1A, KIB3B, KIF26B, MYO5A, MYO9A, BSN
○ Stem-related genes: SOX4, CD164, SOX9
○ TLS(tertiary lymphoid structure) (ref): IGHA1, IGHG1, IGHG2, IGHG3, IGHG4, IGHGP, IGHM, IGKC, IGLC1, IGLC2, IGLC3, JCHAIN, CD79A, FCRL5, MZB1, SSR4, XBP1, TRBC2, IL7R, CXCL12, LUM, C1QA, C7, CD52, APOE, PTLP, PTGDS, PIM2, DERL3
○ TLS(tertiary lymphoid structure) (ref) : CD4, CD8A, CD74, CD79A, IL7R, ITGAE, CD1D, CD3D, CD3E, CD8B, CD19, CD22, CD52, CD79B, CR2, CXCL13, CXCR5, FCER2, MS4A1, PDCD1, PTGDS, TRBC2
○ mitochondrial score (apoptosis score) : mt-Nd1, mt-Nd2, mt-Co1, mt-Co2, mt-Atp8, mt-Atp6, mt-Co3, mt-Nd3, mt-Nd4l, mt-Nd4, mt-Nd5, mt-Nd6, mt-Cytb, MT-ND1, MT-ND2, MT-CO1, MT-CO2, MT-ATP8, MT-ATP6, MT-CO3, MT-ND3, MT-ND4L, MT-ND4, MT-ND5, MT-ND6, MT-CYB
○ hemoglobin score : Hbb-bt, Hbb-bs, Hbb-bh2, Hbb-bh1, Hbb-y, Hba-x, Hba-a1, Hbq1b, Hba-a2, Hbq1a, HBB, HBD, HBG1, HBG2, HBE1, HBZ, HBM, HBA2, HBA1, HBQ1
○ naïveness score : CCR7, TCF7, LEF1, SELL
4. MF(molecular function)
○ Interferon response: IFITM1, NFKBIA, IFI27, IFI30, Cxcl9, Cxcl10, Cd274, IFIT3, MX1, IFI44L, OAS1, CXCL10, ISG20, IFI6, C1R, IFI44, C1S, PARP14, LAP3, PLSCR1, IFI35, TNFSF10, GBP1, IFIT1, SOD2, TAP1, EPSTI1, SCO2, XAF1, APOL2, SERPING1, SAMD9L, IL32, IRF7, RNF213, TAP2, IRF1, ICAM1, OASL, TRIM22, GBP4, ISG15, STAT1, HAPLN3, UBE2L6, PARP9, CXCL9, STAT2, USP18, SP100, OAS3, IFIH1, WARS (ref)
○ Inflammatory cytokine: IL1A, IL1B, CXCL2, CXCL8, CXCL9, CCL4, CCL18, CXCR4, LYZ, IL6, IFNG, NOS2, PTGS2, TNF, CD47, CD274 (PD-L1), GLI1, NFKB1, CCL3, TNF, IRF5, CSF1R, STAB1, NINJ1, JAK3, LITAF, CCL17, CCL21
○ Anti-inflammtory cytokine: CD163, MSR1
○ Neurochemical: Sst, Pvalb, Vip, Reln
○ DNA repair enzyme: APE1, OGG1, UNG
○ human leukocyte antigen(HLA): HLA-DQA1, HLA-DQB1
○ NF-κB signaling pathway: NFKB1, NFKBIA
○ Heat shock and DNA damage related gene: DNAJB1, HSPH1
○ TGFβ signaling pathway: TGFB2, TGFB3, BMP6
○ JAK–STAT signaling pathway: IL1B, IL6, IL10
○ chemokines: CCL2, CCL4, CCL8, CCL7, CXCL1, CXCL10
○ T cell activation: TNFRSF9 (4-1BB), TNFRSF18 (GITR)
○ androgen receptor (AR) target gene score: KLK2, KLK3, FKBP5, NKX3-1
○ mTORC1 activity: RPS6, MLST8
○ chemokine: CCL3, CCL4L2, XCL1, XCL2
○ stress-linked gene : GADD45B, FOS, ATF3, FOSB, IER3, EGR1, JUN, ZFP36, IER2, PPP1R15A, ID2, NR4A1, DUSP2, IRF1, INTS6, KLF4, MYC, NFKBIZ, BRD2, CCNL1, NFKBIA, IER5, MCL1, KLF6, SERTAD1, RSRP1, KCNQ1OT1, BTG2, HEXIM1, PLK2, TOB1, PPP1R10, HES1, CITED2, SOCS3, DNAJB1, RHOB, DUSP1, JUNB, CDKN1A, ZC3H12A, DNAJA1, SGK1, ZFP36L2, IFRD1, CTD-3252C9.4, MYLIP, PMAIP1, CLDN4, JUND, ADM, ID1, ID3, MIDN, GEM, GADD45G, HERPUD1, PHLDA2, ERRFI1, CLK1, RND3, RGS16, NCOA7, CXCL2, CD83 (ref)
○ immune cell-homing signals: CXCL13, CCL3, CCL4, CCL5
○ adhesion between antigen-presenting cell and T cell: ICAM1, LFA-3, LFA-1, CD2
○ co-stimulation between antigen-presenting cell and T cell: CD40L, OX40, 4-1BB, GITR, CD27, ICOS/CD278, CD28
○ checkpoint blockade between antigen-presenting cell and T cell: PD-1, BTLA, TIGIT, TIM-3, LAG-3, CTLA-4
○ NFkB signaling pathway: NFKB2, NFKBIA
○ WNT signaling: Axin2, Celsr2, Lef1, Nkd2, Prickle2, Sfrp1, Sfrp2, Tcf7, Tcf7l1, Tcf7l2, Vangl2, Wnt2, Wnt4, Dkk1, Dkk2, Dkk3, Fzd1, Fzd2, Fzd3, Fzd4, Fzd5, Fzd7, Fzd8
○ Wnt/BMP signaling: Bmp2, Bmp5, Bmp7
○ Notch signaling: Ep300, Fbxw7, Maml1, Notch1, Notch2, Notch3, Notch4, Rbpj, Dll1, Dll4, Jag1, Jag2
○ Tumor suppressor gene: TP53, DCC, ZNF292, HMGN3, UBE2J1
○ epithelial senescence-associated gene: SLPI, SPRR1B, SPRR3, IL1RN, LCN2, C15orf48, SPRR2A, S100A8, S100A9, CXCL17, MALL, SPRR2D, KRT13, PRSS22, RHCG, ANXA1, ERO1A, PDZK1IP1, S100P, CEACAM5, TMPRSS11D, SPRR1A, PVRL4, KRT16, EMP1, RAB11FIP1, LMO7, NDRG2, SPRR2E, SERPINB1, KRT6A, CD24, C19orf33, PSCA, CEACAM6, CLDN4, CLDN7, SDCBP2, MUC4, MXD1, LYPD3, KRT6B, LY6D, CLIC3, GPRC5A, TSPAN1, PRSS8, SRD5A3, CD55, CSTB, LYNX1, APOBEC3A, S100A7, RDH10, MUC1, TMPRSS11E, CDKN1A, PI3, DSC2, NCCRP1, CEACAM1, SAT1, DUSP5, LIPH, CSTA, TMEM40 (ref)
○ oxphos signature: SRM, ATP5G1, AKR1C1, NDUFAB1, C1QBP, NME1, APRT, H2AFZ, COX5A, NUDT8, NDUFA12, LDHB, CHCHD10, FAM195A, MRPS12, CYC1, NQO1, APOA1BP, PRDX2, PHB, CSRP2, MRPL12, MRPL4, C20orf27, MRPS34, DNPH1, PSMB3, PDCD5, LSM4, DCTPP1, NDUFS8, HSD17B10, NUDT1, BOLA3, NAA38 (ref)
○ hypoxia signature : NDRG1, NDUFA4L2, HILPDA, HK2, VEGFA, ADM, ERO1A, ANKRD37, SLC2A1, EGLN3, ERRFI1, SLC6A8, SPRR1B, BHLHE40, IGFBP3, MKNK2, DDIT4, PFKFB3, KDM3A, RHCG, BNIP3L, BNIP3, EDN1, LDHA, C4orf3, PTHLH, PVRL4, FAM210A, FOSL2, PDK1, CXADR, GPI, CLEC2B, RORA, PGK1, GJB2, MAF, GJB6, KDM7A, FAM162A, P4HA1, MT1X, ENO2, NAMPT, KCMF1, ANGPTL4 (ref)
○ partial EMT signature: LAMC2, PLAU, TNFRSF12A, EMP3, S100A2, LAMB3, PTHLH, TGFBI, PHLDA1, NDRG1, LAMA3, ITGA6, ITGA3, IGFBP7, KRT17, CDH3, P4HA2, TPM1, ARPC1B, PDPN, ACTN1, CTSB (ref)
5. Others
○ sequencing low quality signature : MT-CO3, MT-ATP6, MT-ND2, MT-ND5, MT-ND3, MT-ND4, MT-ND1, MT-CO1, MT-ND4L, MT-CO2, MT-CYB, MTRNR2L12, MT-ND6, COL7A1, SYNE2, MTRNR2L8, PLCG2, RNF213, DST, VMP1, POLR2J3, MDM4, TRIM56, MT-ATP8, NEAT1, MALAT1, LINC00969, FAT1, FAT2, MACF1, SMG1, DYNC1H1, ASH1L, PLXNB2, SLC25A37, LAMA5, DSP, HERC2, BIRC6, USP34, UBR5, HSPG2, TUG1, PARP14, MYH9, SUGP2, EIF4G1, DICER1, ABCA13, PLEC, GABPB1-AS1, KMT2C, AGRN, PRRC2B, ATRX, ARGLU1, DDX17, GOLGB1, DLG1, N4BP2L2 (ref)
Input: 2022.06.21 01:02