Human Lung v2 (HLCA) Reference Explorer
Annotation Markers
ann_level_1
| Label | Markers |
|---|---|
| Immune | LCP1, CD53, PTPRC, COTL1, CXCR4, GMFG, FCER1G, LAPTM5, SRGN, CD52 |
| Epithelial | KRT7, PIGR, ELF3, CYB5A, KRT8, KRT19, TACSTD2, MUC1, S100A14, CXCL17 |
| Endothelial | PTRF, CLDN5, AQP1, PECAM1, NPDC1, VWF, GNG11, RAMP2, IGFBP7, CLEC14A |
| Stroma | TPM2, DCN, MGP, SPARC, CALD1, LUM, TAGLN, IGFBP7, COL1A2, C1S |
ann_level_2
| Label | Markers |
|---|---|
| Myeloid | SPI1, LGALS1, COTL1, MS4A6A, SRGN, TYROBP, LYZ, FCER1G, LAPTM5, AIF1 |
| Lymphoid | CD2, GZMA, CD7, CORO1A, IL32, NKG7, CD69, CXCR4, CD3D, CCL5 |
| Alveolar epithelium | S100A14, CXCL17, SEPP1, NAPSA, SFTPD, PEBP4, SLC34A2, CYB5A, SFTA2, SFTA3 |
| Airway epithelium | PERP, IGFBP2, TSPAN1, KIF21A, ELF3, KRT8, KRT19, TACSTD2, GSTA1, CYP4B1 |
| Blood vessels | PTRF, CLDN5, AQP1, PECAM1, NPDC1, VWF, RAMP3, RAMP2, SPARCL1, CLEC14A |
| Fibroblast lineage | BGN, DCN, MGP, SPARC, CALD1, LUM, COL6A1, IGFBP7, COL1A2, C1S |
| Smooth muscle | DES, SOD3, MYL9, ACTA2, MGP, CALD1, TPM1, TAGLN, IGFBP7, TPM2 |
| Submucosal Gland | CCL28, PIP, ZG16B, PIGR, SEC11C, MARCKSL1, SELM, LTF, TCN1, AZGP1 |
| Lymphatic EC | PPFIBP1, GNG11, RAMP2, CCL21, MMRN1, IGFBP7, SDPR, TM4SF1, CLDN5, ECSCR |
| Mesothelium | CEBPD, LINC01133, MRPL33, UPK3B, CFB, SEPP1, EID1, HP, CUX1, MRPS21 |
ann_level_3
| Label | Markers |
|---|---|
| Macrophages | C1QB, C1QA, HLA-DRB1, AIF1, LYZ, CTSZ, CTSL, FCER1G, C1QC, LAPTM5 |
| Innate lymphoid cell NK | GZMA, CD7, CCL4, CST7, NKG7, GNLY, CTSW, CCL5, GZMB, PRF1 |
| AT2 | NAPSA, SFTPD, PEBP4, SLC39A8, SLC34A2, CYB5A, MUC1, S100A14, SFTA2, SFTA3 |
| Basal | KRT15, SFN, IGFBP2, SERPINF1, ADIRF, MT1X, BCAM, KRT5, KRT17, S100A2 |
| EC venous | VWF, MGP, RAMP3, GNG11, RAMP2, SPARCL1, IGFBP7, CLEC14A, ACKR1, PECAM1 |
| T cell lineage | CD69, CORO1A, CXCR4, CD3E, TRBC2, TRAC, CD2, CCL5, IL32, CD3D |
| EC arterial | SPARCL1, SOX17, IFI27, TM4SF1, A2M, CLEC14A, GIMAP7, CRIP2, CLDN5, PECAM1 |
| Fibroblasts | BGN, DCN, MGP, SPARC, CALD1, LUM, COL6A1, IGFBP7, COL1A2, C1S |
| AT1 | SFTA2, CEACAM6, FXYD3, CAV1, TSPAN13, KRT7, ADIRF, HOPX, AGER, EMP2 |
| Multiciliated lineage | SNTN, FAM229B, TMEM231, C5orf49, C12orf75, GSTA1, C11orf97, RP11-356K23.1, CD24, RP11-295M3.4 |
| B cell lineage | TSC22D3, ISG20, IGHA1, CORO1A, IGKC, IGLC2, LTB, CD79A, CD37, MS4A1 |
| Secretory | KRT19, CEACAM6, WFDC2, TACSTD2, CXCL17, BPIFB1, MUC1, CP, KRT7, PIGR |
| SM activated stress response | C11orf96, HES4, PLAC9, FLNA, KANK2, TPM2, PLN, SELM, GPX3, LBH |
| Monocytes | FCER1G, S100A9, S100A12, VCAN, COTL1, S100A8, CD14, LST1, FCN1, AIF1 |
| Submucosal Secretory | CCL28, PIP, ZG16B, PIGR, SEC11C, MARCKSL1, SELM, LTF, TCN1, AZGP1 |
| EC capillary | IFI27, TM4SF1, CLEC14A, CDH5, PECAM1, HYAL2, SPARCL1, EGFL7, CLDN5, AQP1 |
| Lymphatic EC mature | PPFIBP1, GNG11, RAMP2, CCL21, MMRN1, IGFBP7, SDPR, TM4SF1, CLDN5, ECSCR |
| Rare | FOXI1, HEPACAM2, ATP6V1A, EPCAM, KRT7, TMEM61, ASCL3, CLCNKB, SEC11C, CD24 |
| Lymphatic EC differentiating | AKAP12, TFF3, SDPR, CLDN5, TCF4, TFPI, TIMP3, GNG11, CCL21, IGFBP7 |
| Dendritic cells | CORO1A, MS4A6A, ITGB2, GPR183, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DQB1, HLA-DQA1, HLA-DMA |
| Myofibroblasts | CALD1, CYR61, TAGLN, MT1X, PRELP, TPM2, GPX3, CTGF, IGFBP5, SPARCL1 |
| Mast cells | VWA5A, RGS13, C1orf186, HPGDS, CPA3, GATA2, MS4A2, KIT, TPSAB1, TPSB2 |
| Fibromyocytes | NEXN, ACTG2, LMOD1, IGFBP7, PPP1R14A, DES, FLNA, TPM2, PLN, SELM |
| Lymphatic EC proliferating | S100A16, TUBB, HMGN2, COX20, LSM2, HMGN1, ARPC1A, ECSCR, EID1, MARCKS |
ann_level_4
| Label | Markers |
|---|---|
| Alveolar macrophages | HLA-DPB1, HLA-DPA1, CTSZ, ACP5, COTL1, FCER1G, C1QC, LAPTM5, CTSS, HLA-DQA1 |
| NK cells | GZMA, CD7, CCL4, CST7, NKG7, GNLY, CTSW, CCL5, GZMB, PRF1 |
| Suprabasal | PRDX2, KRT19, SFN, TACSTD2, KRT5, LDHB, KRT17, KLK11, S100A2, SERPINB4 |
| Basal resting | CYR61, PERP, IGFBP2, KRT19, KRT5, KRT17, KRT15, S100A2, LAMB3, BCAM |
| EC venous pulmonary | VWF, MGP, GNG11, RAMP2, SPARCL1, IGFBP7, IFI27, CLDN5, ACKR1, AQP1 |
| CD8 T cells | CD8A, CD3E, CCL4, CD2, CXCR4, GZMA, NKG7, IL32, CD3D, CCL5 |
| Peribronchial fibroblasts | IGFBP7, COL1A2, COL3A1, A2M, BGN, DCN, MGP, LUM, MFAP4, C1S |
| CD4 T cells | CORO1A, KLRB1, CD3E, LTB, CXCR4, IL7R, TRAC, IL32, CD2, CD3D |
| Multiciliated | SNTN, FAM229B, TMEM231, C5orf49, C12orf75, GSTA1, C11orf97, RP11-356K23.1, CD24, RP11-295M3.4 |
| Plasma cells | ITM2C, TNFRSF17, FKBP11, IGKC, IGHA1, IGHG1, CD79A, JCHAIN, MZB1, ISG20 |
| Goblet | PI3, TSPAN8, LCN2, MSMB, C3, MUC5AC, CYP2F1, PIGR, CEACAM6, BPIFB1 |
| Club | LCN2, ELF3, KLK11, AKR1C1, CXCL17, KRT7, CYP2F1, GSTA1, TSPAN8, PIGR |
| Classical monocytes | LST1, IL1B, LYZ, COTL1, S100A9, VCAN, S100A8, S100A12, AIF1, FCN1 |
| Interstitial macrophages | LYZ, CD163, TYROBP, LGALS1, CD68, CTSL, EMP3, AIF1, FCER1G, LAPTM5 |
| SMG serous | CCL28, PART1, PIP, S100A1, AZGP1, PIGR, NDRG2, C6orf58, PRB3, RP11-1143G9.4 |
| EC venous systemic | VWF, MGP, GNG11, PLVAP, RAMP2, SPARCL1, IGFBP7, A2M, CLEC14A, ACKR1 |
| Non classical monocytes | PSAP, FCGR3A, FCN1, CORO1A, COTL1, FCER1G, LAPTM5, CTSS, AIF1, LST1 |
| EC general capillary | EPAS1, GNG11, IFI27, TM4SF1, EGFL7, AQP1, VWF, FCN3, SPARCL1, CLDN5 |
| Adventitial fibroblasts | COL6A2, SFRP2, IGFBP7, IGFBP6, COL3A1, C1S, MMP2, MGP, SPARC, COL1A2 |
| EC aerocyte capillary | EMCN, HPGD, IFI27, CA4, EGFL7, AQP1, IL1RL1, SPARCL1, SDPR, CLDN5 |
| Alveolar fibroblasts | LUM, COL6A1, CYR61, C1R, COL1A2, MFAP4, A2M, C1S, ADH1B, GPX3 |
| Neuroendocrine | UCHL1, TFF3, APOA1BP, CLDN3, SEC11C, NGFRAP1, SCG5, HIGD1A, PHGR1, CD24 |
| DC2 | ITGB2, LAPTM5, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DMA, LST1 |
| Transitional Club AT2 | CXCL17, C16orf89, RNASE1, KRT7, SCGB1A1, PIGR, SCGB3A2, KLK11, SFTA1P, FOLR1 |
| DC1 | HLA-DPA1, CPNE3, CORO1A, CPVL, C1orf54, WDFY4, LSP1, HLA-DQB1, HLA-DQA1, HLA-DMA |
| B cells | CD69, CORO1A, LIMD2, BANK1, LAPTM5, CXCR4, LTB, CD79A, CD37, MS4A1 |
| SMG mucous | FKBP11, TCN1, GOLM1, TFF3, PIGR, KLK11, MARCKSL1, CRACR2B, SELM, MSMB |
| AT2 proliferating | CDK1, LSM3, CKS1B, EIF1AX, UBE2C, MRPL14, PRC1, CENPW, EMP2, DHFR |
| Pericytes | MYL9, SPARC, SPARCL1, IGFBP7, COL4A1, GPX3, PDGFRB, CALD1, COX4I2, TPM2 |
| SMG duct | PIP, ZG16B, PIGR, SAA1, MARCKSL1, ALDH1A3, SELM, LTF, RARRES1, AZGP1 |
| Ionocyte | FOXI1, ATP6V1A, GOLM1, TMEM61, SEC11C, SCNN1B, ASCL3, CLCNKB, HEPACAM2, CD24 |
| Deuterosomal | RSPH9, PIFO, RUVBL2, C11orf88, FAM183A, MORN2, SAXO2, CFAP126, FAM229B, C5orf49 |
| Tuft | MUC20, KHDRBS1, ZNF428, BIK, CRYM, LRMP, HES6, KIT, AZGP1, RASSF6 |
| Plasmacytoid DCs | IL3RA, TCF4, LTB, GZMB, JCHAIN, ITM2C, IRF8, PLD4, IRF7, C12orf75 |
| T cells proliferating | TRAC, HMGN2, IL32, CORO1A, ARHGDIB, STMN1, RAC2, IL2RG, HMGB2, CD3D |
| Subpleural fibroblasts | SERPING1, C1R, COL1A2, NNMT, COL3A1, MT1E, MT1X, PLA2G2A, SELM, MT1M |
| Migratory DCs | IL2RG, HLA-DRB5, TMEM176A, BIRC3, TYMP, CCL22, SYNGR2, CD83, LSP1, HLA-DQA1 |
ann_level_5
| Label | Markers |
|---|---|
| Alveolar Mφ CCL3+ | MCEMP1, UPP1, HLA-DQA1, C5AR1, HLA-DMA, AIF1, LST1, LINC01272, MRC1, CCL18 |
| Multiciliated (non-nasal) | SNTN, FAM229B, TMEM231, C5orf49, C12orf75, GSTA1, C11orf97, RP11-356K23.1, CD24, RP11-295M3.4 |
| Goblet (nasal) | KRT7, MUC1, MUC5AC, MSMB, CP, LMO7, LCN2, CEACAM6, BPIFB1, PIGR |
| Club (nasal) | ELF3, C19orf33, KRT8, KRT19, TACSTD2, MUC1, S100A14, CXCL17, PSCA, FAM3D |
| Monocyte derived Mφ | LYZ, ACP5, TYROBP, LGALS1, CD68, AIF1, CTSL, EMP3, FCER1G, LAPTM5 |
| Alveolar Mφ proliferating | H2AFV, STMN1, LSM4, GYPC, PTTG1, KIAA0101, FABP4, CKS1B, UBE2C, HMGN2 |
| Club (non-nasal) | SCGB3A1, CYP2F1, GSTA1, HES4, TSPAN8, TFF3, MSMB, BPIFB1, SCGB1A1, PIGR |
| SMG serous (bronchial) | AZGP1, ZG16B, PIGR, NDRG2, LPO, C6orf58, DMBT1, PRB3, FAM3D, RP11-1143G9.4 |
| Multiciliated (nasal) | RP11-356K23.1, EFHC1, CAPS, ROPN1L, RSPH1, C9orf116, TMEM190, DNALI1, PIFO, ODF3B |
| Goblet (bronchial) | MUC5AC, MSMB, PI3, MDK, ANKRD36C, TFF3, PIGR, SAA1, CP, BPIFB1 |
| Interstitial Mφ perivascular | MRC1, RNASE1, FGL2, RNASE6, HLA-DPA1, GPR183, CD14, HLA-DPB1, MS4A6A, AIF1 |
| Goblet (subsegmental) | MDK, MUC5B, SCGB1A1, CP, C3, TSPAN8, TFF3, MSMB, PIGR, BPIFB1 |
| SMG serous (nasal) | ZG16B, MUC7, C6orf58, PRB3, LTF, LYZ, PRR4, AZGP1, PIGR, RP11-1143G9.4 |
| Alveolar Mφ MT-positive | GSTO1, LGALS1, CTSZ, MT2A, APOC1, CTSL, UPP1, CCL18, FABP4, MT1X |
ann_finest_level
| Label | Markers |
|---|---|
| Alveolar macrophages | MS4A7, C1QA, HLA-DQB1, HLA-DMA, HLA-DPB1, HLA-DPA1, ACP5, C1QC, CTSS, HLA-DQA1 |
| NK cells | GZMA, CD7, CCL4, CST7, NKG7, GNLY, CTSW, CCL5, GZMB, PRF1 |
| AT2 | SEPP1, PGC, NAPSA, SFTPD, SLC34A2, CYB5A, MUC1, S100A14, SFTA2, SFTA3 |
| Alveolar Mφ CCL3+ | MCEMP1, UPP1, HLA-DQA1, C5AR1, HLA-DMA, AIF1, LST1, LINC01272, MRC1, CCL18 |
| Suprabasal | PRDX2, KRT19, SFN, TACSTD2, KRT5, LDHB, KRT17, KLK11, S100A2, SERPINB4 |
| Basal resting | CYR61, PERP, IGFBP2, KRT19, KRT5, KRT17, KRT15, S100A2, LAMB3, BCAM |
| EC venous pulmonary | VWF, MGP, GNG11, RAMP2, SPARCL1, IGFBP7, IFI27, CLDN5, ACKR1, AQP1 |
| CD8 T cells | CD8A, CD3E, CCL4, CD2, CXCR4, GZMA, NKG7, IL32, CD3D, CCL5 |
| EC arterial | SPARCL1, SOX17, IFI27, TM4SF1, A2M, CLEC14A, GIMAP7, CRIP2, CLDN5, PECAM1 |
| Peribronchial fibroblasts | IGFBP7, COL1A2, COL3A1, A2M, BGN, DCN, MGP, LUM, MFAP4, C1S |
| CD4 T cells | CORO1A, KLRB1, CD3E, LTB, CXCR4, IL7R, TRAC, IL32, CD2, CD3D |
| AT1 | SFTA2, CEACAM6, FXYD3, CAV1, TSPAN13, KRT7, ADIRF, HOPX, AGER, EMP2 |
| Multiciliated (non-nasal) | SNTN, FAM229B, TMEM231, C5orf49, C12orf75, GSTA1, C11orf97, RP11-356K23.1, CD24, RP11-295M3.4 |
| Plasma cells | ITM2C, TNFRSF17, FKBP11, IGKC, IGHA1, IGHG1, CD79A, JCHAIN, MZB1, ISG20 |
| Goblet (nasal) | KRT7, MUC1, MUC5AC, MSMB, CP, LMO7, LCN2, CEACAM6, BPIFB1, PIGR |
| Club (nasal) | ELF3, C19orf33, KRT8, KRT19, TACSTD2, MUC1, S100A14, CXCL17, PSCA, FAM3D |
| SM activated stress response | C11orf96, HES4, PLAC9, FLNA, KANK2, TPM2, PLN, SELM, GPX3, LBH |
| Classical monocytes | LST1, IL1B, LYZ, COTL1, S100A9, VCAN, S100A8, S100A12, AIF1, FCN1 |
| Monocyte derived Mφ | LYZ, ACP5, TYROBP, LGALS1, CD68, AIF1, CTSL, EMP3, FCER1G, LAPTM5 |
| Alveolar Mφ proliferating | H2AFV, STMN1, LSM4, GYPC, PTTG1, KIAA0101, FABP4, CKS1B, UBE2C, HMGN2 |
| Club (non-nasal) | SCGB3A1, CYP2F1, GSTA1, HES4, TSPAN8, TFF3, MSMB, BPIFB1, SCGB1A1, PIGR |
| SMG serous (bronchial) | AZGP1, ZG16B, PIGR, NDRG2, LPO, C6orf58, DMBT1, PRB3, FAM3D, RP11-1143G9.4 |
| EC venous systemic | VWF, MGP, GNG11, PLVAP, RAMP2, SPARCL1, IGFBP7, A2M, CLEC14A, ACKR1 |
| Non classical monocytes | PSAP, FCGR3A, FCN1, CORO1A, COTL1, FCER1G, LAPTM5, CTSS, AIF1, LST1 |
| EC general capillary | EPAS1, GNG11, IFI27, TM4SF1, EGFL7, AQP1, VWF, FCN3, SPARCL1, CLDN5 |
| Adventitial fibroblasts | COL6A2, SFRP2, IGFBP7, IGFBP6, COL3A1, C1S, MMP2, MGP, SPARC, COL1A2 |
| Lymphatic EC mature | PPFIBP1, GNG11, RAMP2, CCL21, MMRN1, IGFBP7, SDPR, TM4SF1, CLDN5, ECSCR |
| EC aerocyte capillary | EMCN, HPGD, IFI27, CA4, EGFL7, AQP1, IL1RL1, SPARCL1, SDPR, CLDN5 |
| Smooth muscle | PRKCDBP, NDUFA4L2, MYL9, ACTA2, MGP, CALD1, TPM1, TAGLN, IGFBP7, TPM2 |
| Alveolar fibroblasts | LUM, COL6A1, CYR61, C1R, COL1A2, MFAP4, A2M, C1S, ADH1B, GPX3 |
| Multiciliated (nasal) | RP11-356K23.1, EFHC1, CAPS, ROPN1L, RSPH1, C9orf116, TMEM190, DNALI1, PIFO, ODF3B |
| Goblet (bronchial) | MUC5AC, MSMB, PI3, MDK, ANKRD36C, TFF3, PIGR, SAA1, CP, BPIFB1 |
| Neuroendocrine | UCHL1, TFF3, APOA1BP, CLDN3, SEC11C, NGFRAP1, SCG5, HIGD1A, PHGR1, CD24 |
| Lymphatic EC differentiating | AKAP12, TFF3, SDPR, CLDN5, TCF4, TFPI, TIMP3, GNG11, CCL21, IGFBP7 |
| DC2 | ITGB2, LAPTM5, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DMB, HLA-DQB1, HLA-DQA1, HLA-DMA, LST1 |
| Transitional Club AT2 | CXCL17, C16orf89, RNASE1, KRT7, SCGB1A1, PIGR, SCGB3A2, KLK11, SFTA1P, FOLR1 |
| DC1 | HLA-DPA1, CPNE3, CORO1A, CPVL, C1orf54, WDFY4, LSP1, HLA-DQB1, HLA-DQA1, HLA-DMA |
| Myofibroblasts | CALD1, CYR61, TAGLN, MT1X, PRELP, TPM2, GPX3, CTGF, IGFBP5, SPARCL1 |
| B cells | CD69, CORO1A, LIMD2, BANK1, LAPTM5, CXCR4, LTB, CD79A, CD37, MS4A1 |
| Mast cells | VWA5A, RGS13, C1orf186, HPGDS, CPA3, GATA2, MS4A2, KIT, TPSAB1, TPSB2 |
| Interstitial Mφ perivascular | MRC1, RNASE1, FGL2, RNASE6, HLA-DPA1, GPR183, CD14, HLA-DPB1, MS4A6A, AIF1 |
| SMG mucous | FKBP11, TCN1, GOLM1, TFF3, PIGR, KLK11, MARCKSL1, CRACR2B, SELM, MSMB |
| AT2 proliferating | CDK1, LSM3, CKS1B, EIF1AX, UBE2C, MRPL14, PRC1, CENPW, EMP2, DHFR |
| Goblet (subsegmental) | MDK, MUC5B, SCGB1A1, CP, C3, TSPAN8, TFF3, MSMB, PIGR, BPIFB1 |
| Pericytes | MYL9, SPARC, SPARCL1, IGFBP7, COL4A1, GPX3, PDGFRB, CALD1, COX4I2, TPM2 |
| SMG duct | PIP, ZG16B, PIGR, SAA1, MARCKSL1, ALDH1A3, SELM, LTF, RARRES1, AZGP1 |
| Mesothelium | CEBPD, LINC01133, MRPL33, UPK3B, CFB, SEPP1, EID1, HP, CUX1, MRPS21 |
| SMG serous (nasal) | ZG16B, MUC7, C6orf58, PRB3, LTF, LYZ, PRR4, AZGP1, PIGR, RP11-1143G9.4 |
| Ionocyte | FOXI1, ATP6V1A, GOLM1, TMEM61, SEC11C, SCNN1B, ASCL3, CLCNKB, HEPACAM2, CD24 |
| Alveolar Mφ MT-positive | GSTO1, LGALS1, CTSZ, MT2A, APOC1, CTSL, UPP1, CCL18, FABP4, MT1X |
| Fibromyocytes | NEXN, ACTG2, LMOD1, IGFBP7, PPP1R14A, DES, FLNA, TPM2, PLN, SELM |
| Deuterosomal | RSPH9, PIFO, RUVBL2, C11orf88, FAM183A, MORN2, SAXO2, CFAP126, FAM229B, C5orf49 |
| Tuft | MUC20, KHDRBS1, ZNF428, BIK, CRYM, LRMP, HES6, KIT, AZGP1, RASSF6 |
| Plasmacytoid DCs | IL3RA, TCF4, LTB, GZMB, JCHAIN, ITM2C, IRF8, PLD4, IRF7, C12orf75 |
| T cells proliferating | TRAC, HMGN2, IL32, CORO1A, ARHGDIB, STMN1, RAC2, IL2RG, HMGB2, CD3D |
| Subpleural fibroblasts | SERPING1, C1R, COL1A2, NNMT, COL3A1, MT1E, MT1X, PLA2G2A, SELM, MT1M |
| Lymphatic EC proliferating | S100A16, TUBB, HMGN2, COX20, LSM2, HMGN1, ARPC1A, ECSCR, EID1, MARCKS |
| Migratory DCs | IL2RG, HLA-DRB5, TMEM176A, BIRC3, TYMP, CCL22, SYNGR2, CD83, LSP1, HLA-DQA1 |