Gene Score Library
Recommendation: 【Bioinformatics】 Bioinformatics Index
1. Overview
2. BP
3. CC
4. MF
a. Gene Library
1. Overview
○ For other information, see https://www.scinapse.io/, https://typeset.io/, which curated billions of papers.
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
○ Genes that express high in the S phase during the cell cycle: ABHD10, CCDC14, CDKN2AIP, NT5DC1, SVIP, PTAR1
○ Genes that express high in the G2 phase during the cell cycle: ANKRD36C, YEATS4, DCTPP1
○ Genes that express high in the G2/M phase during the cell cycle: SMC4, TMPO, LMNB1, HINT3
○ Genes that express high in the M phase during the cell cycle: HMG20B, HMGB3, HPS4
○ Genes that express high in the G0 phase during the cell cycle: CDKN1A, CDKN1B, CDKN1C
○ 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
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): 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
○ 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
4. MF(molecular function)
○ Interferon response: IFI6, ISG15, IFIT1, IFITM1, NFKBIA, IFI27, IFI30, Cxcl9, Cxcl10, Cd274, STAT1, ISG20
○ 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: JUN, JUNB, FOS
○ 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
Input: 2022.06.21 01:02