Single-Cell Gene Sets

practice

single-cell

Published

May 7, 2026

Purpose

This page collects common gene sets used in single-cell practice notes.

Gene sets here are not always cell-type markers. Some are QC-related sets, some are cell-cycle signatures, some are pattern-based feature groups, and some are cell type marker sets.

Index

Name	Category	Source	Added	Note
S Phase	cell-cycle	Seurat cell-cycle gene sets	2026-05-07	S phase scoring genes
G2M Phase	cell-cycle	Seurat cell-cycle gene sets	2026-05-07	G2/M phase scoring genes
Mitochondrial Genes	QC	pattern-based	2026-05-07	Human `^MT-`; mouse `^mt-`
Hemoglobin Genes	QC	marker genes	2026-05-07	Blood or red blood cell contamination check
Ribosomal Genes	QC	pattern-based	2026-05-07	`RPL` and `RPS` genes
Tirosh 2016 Melanoma Non-Malignant Markers	cell-type markers	Tirosh et al. 2016	2026-05-20	Broad non-malignant melanoma compartments
Human Liver snRNA-seq Markers	cell-type markers	Gribben et al. 2024	2026-05-07	Human liver snRNA-seq cell type markers
Human PBMC 22 Marker Set	cell-type markers	Diaz-Mejia 2019	2026-05-07	PBMC immune cell marker panel

Cell Cycle

S Phase

S phase genes from Seurat cell-cycle gene sets:

s_genes <- c(
  "MCM5", "PCNA", "TYMS", "FEN1", "MCM2", "MCM4",
  "RRM1", "UNG", "GINS2", "MCM6", "CDCA7", "DTL",
  "PRIM1", "UHRF1", "MLF1IP", "HELLS", "RFC2", "RPA2",
  "NASP", "RAD51AP1", "GMNN", "WDR76", "SLBP", "CCNE2",
  "UBR7", "POLD3", "MSH2", "ATAD2", "RAD51", "RRM2",
  "CDC45", "CDC6", "EXO1", "TIPIN", "DSCC1", "BLM",
  "CASP8AP2", "USP1", "CLSPN", "POLA1", "CHAF1B", "BRIP1",
  "E2F8"
)

G2M Phase

G2M phase genes from Seurat cell-cycle gene sets:

g2m_genes <- c(
  "HMGB2", "CDK1", "NUSAP1", "UBE2C", "BIRC5", "TPX2", "TOP2A",
  "NDC80", "CKS2", "NUF2", "CKS1B", "MKI67", "TMPO", "CENPF",
  "TACC3", "FAM64A", "SMC4", "CCNB2", "CKAP2L", "CKAP2", "AURKB",
  "BUB1", "KIF11", "ANP32E", "TUBB4B", "GTSE1", "KIF20B", "HJURP",
  "CDCA3", "HN1", "CDC20", "TTK", "CDC25C", "KIF2C", "RANGAP1",
  "NCAPD2", "DLGAP5", "CDCA2", "CDCA8", "ECT2", "KIF23", "HMMR",
  "AURKA", "PSRC1", "ANLN", "LBR", "CKAP5", "CENPE", "CTCF",
  "NEK2", "G2E3", "GAS2L3", "CBX5", "CENPA"
)

QC Gene Sets

Mitochondrial Genes

Mitochondrial genes are usually selected by pattern.

Human:

human_mito_pattern <- "^MT-"

Mouse:

mouse_mito_pattern <- "^mt-"

Hemoglobin Genes

Hemoglobin genes are useful for checking red blood cell or blood contamination.

hb_genes <- c(
  "HBA1", "HBA2", "HBB", "HBD", "HBE1",
  "HBG1", "HBG2", "HBM", "HBQ1", "HBZ"
)

Ribosomal Genes

Ribosomal protein genes are usually selected by pattern rather than a short fixed list.

ribo_genes <- grep(
  pattern = "^RP[SL]",
  x = rownames(seu),
  value = TRUE,
  ignore.case = TRUE
)

This matches RPL* and RPS* genes found in the object.

Cell Type Marker Sets

Cell type marker sets are named lists. Each element is one cell type or cell state, and each value is a character vector of marker genes.

These marker sets are reusable gene sets. They can be used for manual annotation, marker checking, module scoring, or marker-signature-based annotation.

Tirosh 2016 Melanoma Non-Malignant Markers

Markers used by Tirosh et al. 2016 to annotate broad non-malignant cell compartments in metastatic melanoma scRNA-seq. This is a historical paper-specific marker set, recorded for reading and reproduction context rather than as a current best-practice annotation panel.

melanoma_tirosh2016_nonmalignant_markers <- list(
  "T cells" = c("CD2", "CD3D", "CD3E", "CD3G"),
  "B cells" = c("CD19", "CD20", "CD79A", "CD79B", "BLNK"),
  "Macrophages" = c("CD14", "CD68", "CD163", "CSF1R"),
  "Endothelial cells" = c("PECAM1", "VWF", "CDH5", "SELE"),
  "CAFs" = c("FAP", "CD90", "COL1A1", "COL3A1"),
  "pDCs" = c("CD123", "CD303", "CD304"),
  "NK cells" = c("CD16", "CD56", "KLRB1", "KLRC1", "KLRD1", "KLRF1", "KLRK1")
)

Human Liver snRNA-seq Markers

Markers from Gribben et al., Nature (2024), doi:10.1038/s41586-024-07465-2.

liver_snrna_gribben2024_markers <- list(
  "Hepatocytes" = c(
    "ALB", "ASGR1", "AL391117.1", "TFR2", "APOC1", "ADH4",
    "HPX", "C3", "FGB", "PLG", "FYB2", "APOB", "GHR",
    "TENM2", "CYP3A4", "CYP3A7"
  ),
  "Cholangiocytes" = c("CFTR", "BICC1", "PKHD1", "CTNND2", "RAYL"),
  "Stellate cells" = c(
    "DCN", "COL3A1", "PTH1R", "ADAMTSL2", "CCBE1",
    "ADAMTS2", "ADAMTSL1"
  ),
  "Endothelial" = c("KDR", "FCN3", "FLT1", "OIT3", "STAB2", "TEK", "PTPRB", "FCN2"),
  "Lymphocytes" = c("IL7R", "CD96", "BCL11B", "THEMIS", "CD247", "PTPRC"),
  "Macrophages" = c("NDST3", "MARCO", "CD163", "MSR1", "GAS7", "CD5L"),
  "Neutrophils" = c("FCN1"),
  "B cells 1" = c("BANK1", "PAX5", "IGKC"),
  "B cells 2" = c("IGKC", "FCRL5")
)

Human PBMC 22 Marker Set

Markers from Diaz-Mejia 2019, Zenodo DOI:10.5281/zenodo.3369934.

pbmc_22_10x_markers <- list(
  "B_CELLS_MEMORY" = c(
    "AIM2", "BANK1", "BLK", "CD19", "CD27", "CD37", "CD69",
    "CD79A", "CD79B", "FAIM3", "FAM65B", "FCGR2B", "FCRL2",
    "GUSBP11", "HLA-DOB", "IGHM", "IGKC", "IGLL3P", "IRF8",
    "KIAA0226L", "LTB", "LY86", "MS4A1", "P2RX5", "PNOC",
    "PTPRCAP", "RASGRP2", "SELL", "SIK1", "SPIB"
  ),
  "B_CELLS_NAIVE" = c(
    "BACH2", "BANK1", "CCR7", "CD19", "CD22", "CD37", "CD69",
    "CD79A", "CD79B", "EAF2", "FAIM3", "FAM65B", "FCGR2B",
    "FCRL2", "GPR18", "GUSBP11", "HHEX", "HLA-DOB", "IGHD",
    "IGHM", "IGKC", "IGLL3P", "IL4R", "IRF8", "KIAA0226L",
    "LTB", "LY86", "MS4A1", "P2RX5", "PNOC", "PTPRCAP",
    "RASGRP2", "SELL", "SIK1", "SPIB", "STAP1", "TCL1A", "VPREB3"
  ),
  "DENDRITIC_CELLS_ACTIVATED" = c(
    "ACP5", "BCL2A1", "BIRC3", "CCL13", "CCL17", "CCL19",
    "CCL22", "CCL4", "CCL5", "CCR7", "CD38", "CD40", "CD80",
    "CD86", "CHST7", "CLIC2", "CST7", "CXCL10", "CXCL11",
    "EBI3", "FPR3", "HCK", "HLA-DQA1", "IDO1", "IFI44L",
    "IL7R", "KYNU", "LAMP3", "MMP12", "NCF2", "PLA2G7",
    "RGS1", "RSAD2", "SAMSN1", "SLC15A3", "TNFAIP6"
  ),
  "DENDRITIC_CELLS_RESTING" = c(
    "ACP5", "AIF1", "C1ORF54", "CCL13", "CCL22", "CD1A",
    "CD1B", "CD1C", "CD1E", "CLEC10A", "CLEC4A", "CLEC7A",
    "EGR2", "FPR3", "HCK", "HLA-DQA1", "IGSF6", "LST1",
    "MMP12", "MMP9", "MNDA", "MS4A6A", "NCF2", "PLA2G7",
    "RNASE6", "SLC15A3", "TREM2"
  ),
  "EOSINOPHILS" = c(
    "BCL2A1", "C3AR1", "CCL4", "CCR3", "CD69", "CLC",
    "DPEP2", "EMR1", "EMR2", "EMR3", "FOSB", "FPR1",
    "GPR183", "GPR65", "GPR97", "HCK", "LRMP", "LST1",
    "MNDA", "MYB", "NCF2", "NR4A3", "P2RY14", "RGS1",
    "RNASE2", "SAMSN1", "SELL", "ZNF165"
  ),
  "MACROPHAGES_M0" = c(
    "ACP5", "ADAMDEC1", "AQP9", "BCL2A1", "BHLHE41", "C5AR1",
    "CHI3L1", "CLEC7A", "CXCL5", "CYP27A1", "DCSTAMP",
    "EGR2", "FPR3", "HCK", "HK3", "IGSF6", "IL7R", "KYNU",
    "MMP9", "NCF2", "PLA2G7", "PPBP", "SLC15A3"
  ),
  "MACROPHAGES_M1" = c(
    "ADAMDEC1", "APOBEC3A", "APOL3", "AQP9", "BCL2A1",
    "C3AR1", "CCL19", "CCL4", "CCL5", "CCL8", "CCR7",
    "CD38", "CD40", "CD80", "CHI3L1", "CXCL10", "CXCL11",
    "CXCL9", "CYP27B1", "EBI3", "EMR1", "HCK", "HLA-DQA1",
    "IDO1", "IFI44L", "IL2RA", "IL4R", "IRF8", "KYNU",
    "LAMP3", "LILRB2", "MNDA", "RASSF4", "RSAD2", "SAMSN1",
    "SIGLEC1", "SLAMF1", "SLC15A3", "SLC2A6", "TLR2", "TNFAIP6"
  ),
  "MACROPHAGES_M2" = c(
    "ACP5", "ADAMDEC1", "AIF1", "CCL13", "CCL18", "CCL23",
    "CCL4", "CD4", "CLEC10A", "CLEC4A", "CLEC7A", "HCK",
    "HLA-DQA1", "IRF8", "LY86", "MMP9", "MS4A6A", "NCF2",
    "NPL", "RNASE6", "SAMSN1", "SIGLEC1", "SLC15A3", "TLR2", "TREM2"
  ),
  "MAST_CELLS_ACTIVATED" = c(
    "BCL2A1", "C3AR1", "CCL20", "CCL4", "CLC", "CPA3",
    "CTSG", "CXCL3", "ELANE", "FCER1A", "GZMB", "HDC",
    "HPGDS", "IL1B", "IL4R", "MMP9", "MYB", "PRG2", "RGS13",
    "SAMSN1", "TPSAB1"
  ),
  "MAST_CELLS_RESTING" = c(
    "ADRB2", "C3AR1", "CLC", "CPA3", "CTSG", "ELANE",
    "FCER1A", "HDC", "HPGDS", "IL1B", "IL4R", "LAT",
    "MS4A2", "MYB", "PRG2", "SAMSN1", "STAP1", "TPSAB1"
  ),
  "MONOCYTES" = c(
    "AIF1", "C5AR1", "CCL4", "CD37", "CD4", "CFP", "CHST15",
    "CLEC7A", "FCN1", "FOSB", "FPR1", "HCK", "HK3", "LILRB2",
    "LST1", "LY86", "MNDA", "MS4A6A", "NCF2", "RNASE2",
    "RNASE6", "S100A12", "SELL", "TLR2", "VNN2"
  ),
  "NEUTROPHILS" = c(
    "AIF1", "APOBEC3A", "AQP9", "BCL2A1", "C5AR1", "CD300A",
    "CD37", "CDA", "CHI3L1", "CHST15", "CLC", "CLEC7A",
    "CSF3R", "CXCR1", "CXCR2", "DPEP2", "EMR2", "EMR3",
    "FAM65B", "FCGR3B", "FCN1", "FFAR2", "FPR1", "FPR2",
    "HAL", "HCK", "HSPA6", "IGSF6", "IL1B", "LRMP", "LST1",
    "LTB", "MGAM", "MMP25", "MMP9", "MNDA", "NCF2", "P2RY13",
    "QPCT", "S100A12", "SELL", "TLR2", "TNFAIP6", "TNFRSF10C",
    "TREM1", "VNN2"
  ),
  "NK_CELLS_ACTIVATED" = c(
    "APOBEC3G", "CCL4", "CCL5", "CCND2", "CD2", "CD247",
    "CD300A", "CD69", "CST7", "CTSW", "GNLY", "GZMA",
    "GZMB", "GZMH", "IFNG", "IL18RAP", "IL2RB", "ITK",
    "KIR2DS4", "KLRB1", "KLRD1", "KLRF1", "KLRK1", "LTB",
    "NCR3", "NKG7", "PRF1", "PTGER2", "PTPRCAP", "PVRIG",
    "TBX21", "TRDC"
  ),
  "NK_CELLS_RESTING" = c(
    "APOBEC3G", "CCL4", "CCL5", "CD2", "CD247", "CD300A",
    "CST7", "CTSW", "DEFA4", "GNLY", "GZMA", "GZMB", "GZMH",
    "GZMM", "IL18RAP", "IL2RB", "ITK", "KLRB1", "KLRD1",
    "KLRF1", "KLRK1", "LCK", "NKG7", "PRF1", "PTPRCAP",
    "PVRIG", "SELL", "TBX21", "TRBC1", "TRDC", "ZAP70"
  ),
  "PLASMA_CELLS" = c(
    "AMPD1", "CD27", "CD38", "CD79A", "EAF2", "GUSBP11",
    "HLA-DOB", "IGHD", "IGHE", "IGHM", "IGKC", "IGLL3P",
    "LOC100130100", "MAN1A1", "MZB1", "PNOC", "RASGRP3",
    "SIK1", "SPAG4", "TNFRSF17"
  ),
  "T_CELLS_CD4_MEMORY_ACTIVATED" = c(
    "AIM2", "CCL4", "CD2", "CD3D", "GZMB", "IFNG", "IL2RA",
    "IL2RB", "IL9", "ITK", "LCK", "LTB", "TRAC", "TRBC1"
  ),
  "T_CELLS_CD4_MEMORY_RESTING" = c(
    "BCL11B", "CCL5", "CD2", "CD247", "CD27", "CD37", "CD3D",
    "CD3E", "CD3G", "CD4", "CD6", "CD69", "FAIM3", "GPR183",
    "GZMA", "GZMK", "IL7R", "ITK", "KLRB1", "LAT", "LCK",
    "LTB", "PBXIP1", "PIK3IP1", "PTGER2", "PTPRCAP", "RPL3P7",
    "SELL", "SPOCK2", "TCF7", "TRAC", "TRBC1", "ZFP36L2"
  ),
  "T_CELLS_CD4_NAIVE" = c(
    "ATHL1", "BCL11B", "CCR7", "CD2", "CD247", "CD27",
    "CD3D", "CD3E", "CD69", "DGKA", "FAIM3", "FAM65B",
    "IL7R", "ITK", "LAT", "LCK", "LTB", "PIK3IP1", "RASGRP2",
    "RPL3P7", "SELL", "TCF7", "TRAC", "TRBC1", "ZAP70"
  ),
  "T_CELLS_CD8" = c(
    "BCL11B", "CCL5", "CCR7", "CD2", "CD247", "CD27", "CD37",
    "CD3D", "CD3E", "CD3G", "CD69", "CD8A", "CD8B", "CST7",
    "CTSW", "DUSP2", "FAIM3", "FAM65B", "GNLY", "GZMA", "GZMH",
    "GZMK", "IGKC", "IL2RB", "IL7R", "ITK", "KLRB1", "KLRG1",
    "KLRK1", "LAT", "LCK", "LTB", "NKG7", "PIK3IP1", "PRF1",
    "PTPRCAP", "PVRIG", "SELL", "SPOCK2", "TCF7", "TRAC",
    "TRBC1", "TRDC", "ZAP70", "ZFP36L2"
  ),
  "T_CELLS_FOLLICULAR_HELPER" = c(
    "BCL11B", "CD2", "CD247", "CD27", "CD37", "CD3D", "CD4",
    "CD69", "CHI3L2", "CXCL13", "DGKA", "FAIM3", "FOSB",
    "ICOS", "IL2RB", "IL7R", "ITK", "KLRB1", "LAT", "LCK",
    "LTB", "MAP4K1", "PASK", "PTPRCAP", "PVRIG", "SELL",
    "SIK1", "SIRPG", "SPOCK2", "TCF7", "TRAC", "TRBC1",
    "TRIB2", "ZAP70"
  ),
  "T_CELLS_GAMMA_DELTA" = c(
    "APOBEC3G", "CCL4", "CCL5", "CD160", "CD2", "CD247",
    "CD3D", "CD69", "CD96", "CST7", "CTSW", "DUSP2", "FCN1",
    "GNLY", "GPR171", "GZMA", "GZMB", "GZMH", "GZMK", "IL18RAP",
    "IL2RB", "ITK", "KLRB1", "KLRD1", "KLRF1", "KLRG1",
    "KLRK1", "LCK", "LTB", "NKG7", "PRF1", "PVRIG", "SELL",
    "TRAC", "TRBC1", "TRDC"
  ),
  "T_CELLS_REGULATORY_TREGS" = c(
    "CCR7", "CD2", "CD247", "CD27", "CD37", "CD3D", "CD3E",
    "CD4", "CD5", "CD7", "CTLA4", "FAIM3", "GPR171", "IFI44L",
    "IL2RA", "IL2RB", "IL4R", "ITK", "LAIR2", "LAT", "LCK",
    "LTB", "PBXIP1", "PIK3IP1", "PMCH", "PTPRCAP", "SELL",
    "SIT1", "SKAP1", "SPOCK2", "TRAC", "TRBC1"
  )
)

Note

This page is a reference for reusable gene sets. Pages such as QC or cell-cycle scoring should explain how the gene sets are used in a workflow.