【생물정보학】 유전자 스코어 라이브러리

유전자 스코어 라이브러리(gene score library)

 

추천글 : 【생물정보학】 생물정보학 분석 목차  

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1. 개요 [본문]

2. BP [본문]

3. CC [본문]

4. MF [본문]

5. 기타 [본문]

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a. 유전자 라이브러리 

b. 셀 타입 마커 유전자

c. 리간드-수용체 상호작용 데이터베이스

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1. 개요 [목차]

○ 기타 부족한 정보는 수십억 개의 논문을 큐레이션 한 https://typeset.io/, https://www.scinapse.io/를 참고할 수 있음

 

 

2. BP(biological process) [목차]

○ 섬유화(fibrosis) 마커 : COL1A1, COL3A1, COL5A1, SPP1, FN1, POSTN, FGF1, PDGFB, CTGF, FGF7, IL34, CDC42, CXCL12 (SDF1), TGFBR1, TGFBR2, CCL3, CCL4, COL5A2, ADIPOQ

○ 코로나 바이러스 침투 경로 : ACE2, TMPRSS2, PCK5, PCSK7, CTSL, CTSB, NRP1

○ 저산소증 관련 스코어 : DCN, DDIT4, PRKCA, NDRG1

○ 세포주기 중 G1/S기에 높게 발현하는 유전자 

○ 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)

○ 세포주기 중 S기에 높게 발현하는 유전자 : ABHD10, CCDC14, CDKN2AIP, NT5DC1, SVIP, PTAR1 (ref)

○ 세포주기 중 G2기에 높게 발현하는 유전자 : ANKRD36C, YEATS4, DCTPP1 (ref)

○ 세포주기 중 G2/M기에 높게 발현하는 유전자 

○ 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)

○ 세포주기 중 M기에 높게 발현하는 유전자 : HMG20B, HMGB3, HPS4 (ref)

○ 세포주기 중 G0기에 높게 발현하는 유전자 : CDKN1A, CDKN1B, CDKN1C (ref)

○ 세포주기 관련 스코어 : CDC20, CCNB1, CENPF, PTTG1

○ 세포 성장 조절 : AREG, EGR1

○ 혈관 리모델링(vascular remodeling) : VEGFB, VEGFC, ANGPTL4

○ 타입 1 immunity : CCL3, CXCL9, CXCL10, CXCL11, IL18

○ 타입 2 immunity : CCL11, CCL13, CD5L, IL4, IL5, IL13, IL24

○ 면역 활성화 : CD40LG, CD48, CD80, CD86

○ 전이(metastasis) 관련 유전자 : PLAU, PLAUR, RELB, AREG

○ 면역 관문(immune checkpoint) 관련 유전자 : HAVCR2, CD47, LGALS9, CD276, LAG3, PDCD1, BTLA, CD274 (PD-L1), PDCD1LG2 (PD-L2), VSIR, MIF, SIGLEC10, CTLA4, TIGIT, CD96, TNFRSF1B

○ 증식(proliferation) 관련 유전자 : MKI67, MCM2, PCNA, STMN1, Mki67, Mpp1

○ 면역 억제(immunosuppression) : APOE, GPNMB

○ E2F 타겟 : ATAD2, MCM2, BIRC5

○ 신경 분화 : STMN2, STMN4, TUBB3

○ 항원 제시(antigen presentation) : CD74, HLA-DRB1, HLA-DQA2, HLA-C, HLA-DRB5

○ antigen processing : LY75, TAP1

○ migratory marker : CCR7, CCL19

○ 케라틴화(keratinization) : SPRR2D, SPRR2E, SPRR2A, CRCT1, CNFN

○ 세포자연사(cell apoptosis) : FOXO3, MCL1

○ malignancy score : KRT18, IRX2, NAPSA, SPINK13, KRT7, CAPN8, GPRC5A

○ 면역 반응(immune response) : STAT4, MYB

 

 

3. CC(cellular component) [목차]

○ 보체 활성화(complement activation) : C1QA, C1QB, C1QC, CFD, C7

○ 면역 글로불린(immunoglobulin) : IGKC, IGKV4-1, IGHA1, IGHG2, IGLV9-49, IGHV1-46

○ 세포외 기질(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 세포 수용체(TCR) : TRAC, TRBC, TRDC, Cd3e, Cd4, Cd8a

○ MHC 분자 : HLA-DRA, HLA-DPA1, HLA-C, HLA-DRB5, HLA-DQA2

○ MHC Class II : H2-ab1, H2-aa, H2-eb1

○ 멜라닌 생성 및 패키징 : Tyrp1, Dct, Pmel, Mlana

○ 글루탐산염 수용체 : GRIK1, GRIK3, GRIK5

○ 전압 의존성 포타슘 채널 : KCND3, KCNK1, KCNMA1, KCNQ2, KCNT1

○ 전압 의존성 칼슘 채널 : CACNA1A, CACNA1C, CACNA2D1

○ 미세소관 배열 및 수송 : DYNC2LI1, KIF3A, CFAPs, IFTs, MCTL1

○ 시냅스 소포 전달 및 방출 : KIF1A, KIB3B, KIF26B, MYO5A, MYO9A, BSN

○ 줄기세포 관련 유전자 : 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) [목차]

○ 인터페론 반응(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)

○ 염증성 사이토카인(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

○ 항염증성 사이토카인(anti-inflammatory cytokine) : CD163, MSR1 

○ 신경 화학 물질(neurochemical) : Sst, Pvalb, Vip, Reln

○ DNA repair enzyme : APE1, OGG1, UNG

○ HLA(human leukocyte antigen) : HLA-DQA1, HLA-DQB1

○ NF-κB 신호전달 경로 : NFKB1, NFKBIA

○ 열 충격 및 DNA damage 연관 유전자 : DNAJB1, HSPH1

○ TGFβ 신호전달 경로 : TGFB2, TGFB3, BMP6

○ JAK-STAT 신호전달 경로 : IL1B, IL6, IL10

○ chemokine : CCL2, CCL4, CCL8, CCL7, CXCL1, CXCL10

○ T cell activation : TNFRSF9 (4-1BB), TNFRSF18 (GITR)

○ 안드로젠 수용체(AR)의 타겟 유전자 스코어 : KLK2, KLK3, FKBP5, NKX3-1

○ mTORC1 activity : RPS6, MLST8

○ 케모카인(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 signal : CXCL13, CCL3, CCL4, CCL5

○ 항원제시세포와 T cell 간 adhesion : ICAM1, LFA-3, LFA-1, CD2

○ 항원제시세포와 T cell 간 co-stimulation : CD40L, OX40, 4-1BB, GITR, CD27, ICOS/CD278, CD28

○ 항원제시세포와 T cell 간 checkpoint blockade : PD-1, BTLA, TIGIT, TIM-3, LAG-3, CTLA-4

○ NFkB 신호전달 경로 : NFKB2, NFKBIA

○ WNT 시그널링 : 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 시그널링 : Bmp2, Bmp5, Bmp7

○ Notch 시그널링 : Ep300, Fbxw7, Maml1, Notch1, Notch2, Notch3, Notch4, Rbpj, Dll1, Dll4, Jag1, Jag2

○ 종양 억제 유전자(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. 기타 [목차]

○ 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)

 

입력: 2022.06.21 01:02

수정: 2024.02.20 00:42