Popular Vote (popV) model for automated cell type annotation of single-cell RNA-seq data. We provide here pretrained models for plug-in use in your own analysis. Follow our tutorial to learn how to use the model for cell type annotation.

Model description

Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues.

Link to CELLxGENE: Link to the data in the CELLxGENE browser for interactive exploration of the data and download of the source data.

Training Code URL: Not provided by uploader.

Metrics

We provide here accuracies for each of the experts and the ensemble model. The validation set accuracies are computed on a 10% random subset of the data that was not used for training.

Cell Type N cells celltypist knn bbknn knn harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
B cell 11445 0.99 0.99 0.99 0.99 0.00 0.98 0.98 0.98 0.99
CD4-positive, alpha-beta T cell 9766 0.57 0.78 0.82 0.75 0.00 0.51 0.43 0.49 0.79
fibroblast 8344 0.79 0.79 0.94 0.70 0.00 0.60 0.65 0.64 0.89
CD8-positive, alpha-beta T cell 7611 0.71 0.78 0.81 0.74 0.00 0.76 0.57 0.62 0.80
neutrophil 6846 0.95 0.97 0.97 0.97 0.00 0.95 0.95 0.94 0.98
macrophage 6948 0.80 0.84 0.92 0.80 0.00 0.75 0.73 0.71 0.89
stromal cell of ovary 3441 0.94 0.94 0.91 0.66 0.00 0.50 0.96 0.92 0.97
endothelial cell 3271 0.67 0.74 0.91 0.62 0.00 0.52 0.71 0.64 0.83
basal cell 3333 0.84 0.85 0.89 0.69 0.00 0.64 0.87 0.83 0.93
plasma cell 2645 0.97 0.98 0.97 0.98 0.00 0.98 0.98 0.97 0.99
bladder urothelial cell 2720 0.96 0.97 0.97 0.58 0.00 0.46 0.98 0.97 0.98
monocyte 2566 0.47 0.37 0.78 0.45 0.00 0.24 0.50 0.54 0.62
mesenchymal stem cell 2321 0.84 0.83 0.90 0.42 0.00 0.01 0.89 0.82 0.93
smooth muscle cell 1764 0.67 0.67 0.88 0.67 0.00 0.67 0.74 0.73 0.80
classical monocyte 1837 0.52 0.62 0.77 0.43 0.00 0.56 0.58 0.67 0.73
luminal epithelial cell of mammary gland 1592 0.98 0.03 0.96 0.66 0.00 0.68 0.98 0.97 0.99
capillary endothelial cell 1532 0.67 0.69 0.87 0.58 0.00 0.52 0.71 0.67 0.79
erythrocyte 1495 0.97 0.96 0.95 0.97 0.00 0.97 0.96 0.96 0.97
natural killer cell 1434 0.74 0.74 0.74 0.70 0.00 0.74 0.68 0.70 0.76
enterocyte of epithelium proper of duodenum 1402 0.90 0.34 0.81 0.40 0.00 0.00 0.91 0.89 0.95
stratified squamous epithelial cell 1259 0.82 0.78 0.89 0.67 0.00 0.66 0.85 0.81 0.89
acinar cell of salivary gland 1236 0.88 0.82 0.94 0.53 0.00 0.36 0.94 0.92 0.97
pulmonary alveolar type 2 cell 1184 0.94 0.96 0.97 0.77 0.00 0.69 0.96 0.95 0.98
conjunctival epithelial cell 1154 0.92 0.75 0.86 0.57 0.00 0.31 0.95 0.88 0.95
pericyte 1066 0.56 0.55 0.81 0.54 0.00 0.56 0.61 0.66 0.74
luminal cell of prostate epithelium 1064 0.90 0.81 0.93 0.65 0.00 0.52 0.95 0.92 0.96
cardiac endothelial cell 1038 0.94 0.91 0.93 0.50 0.00 0.18 0.95 0.89 0.96
naive thymus-derived CD4-positive, alpha-beta T cell 982 0.23 0.02 0.32 0.07 0.00 0.24 0.22 0.29 0.27
kidney epithelial cell 882 0.98 0.92 0.95 0.45 0.00 0.59 0.99 0.98 0.99
hepatocyte 695 0.99 0.99 0.96 0.68 0.00 0.67 1.00 0.96 0.99
blood vessel smooth muscle cell 665 0.68 0.50 0.90 0.46 0.00 0.11 0.89 0.79 0.92
enterocyte of epithelium proper of ileum 648 0.93 0.01 0.70 0.26 0.00 0.00 0.97 0.93 0.96
T cell 670 0.42 0.22 0.58 0.16 0.00 0.28 0.34 0.39 0.55
mast cell 601 0.86 0.86 0.96 0.83 0.00 0.84 0.91 0.87 0.94
skeletal muscle satellite stem cell 577 0.85 0.92 0.96 0.83 0.00 0.80 0.94 0.91 0.96
regular atrial cardiac myocyte 561 0.82 0.63 0.78 0.19 0.00 0.27 0.87 0.90 0.90
pancreatic acinar cell 535 0.95 0.32 0.94 0.42 0.00 0.02 0.98 0.95 0.98
intermediate monocyte 554 0.30 0.15 0.58 0.26 0.00 0.22 0.36 0.47 0.53
mature NK T cell 547 0.43 0.40 0.54 0.33 0.00 0.46 0.35 0.42 0.57
mononuclear phagocyte 543 0.44 0.00 0.90 0.14 0.00 0.13 0.66 0.50 0.71
fibroblast of breast 532 0.93 0.00 0.95 0.40 0.00 0.48 0.85 0.63 0.94
vascular associated smooth muscle cell 526 0.66 0.04 0.74 0.18 0.00 0.42 0.61 0.64 0.71
vein endothelial cell 487 0.34 0.17 0.76 0.33 0.00 0.35 0.47 0.45 0.57
CD4-positive, alpha-beta thymocyte 503 0.38 0.00 0.61 0.23 0.00 0.25 0.40 0.38 0.59
enterocyte of epithelium of large intestine 437 0.69 0.27 0.58 0.33 0.00 0.25 0.80 0.83 0.79
myofibroblast cell 428 0.50 0.22 0.85 0.40 0.00 0.46 0.63 0.55 0.77
thymic fibroblast type 2 434 0.54 0.00 0.73 0.14 0.00 0.06 0.66 0.55 0.62
corneal epithelial cell 405 0.92 0.00 0.92 0.55 0.00 0.59 0.94 0.91 0.95
spermatid 416 0.91 0.00 0.96 0.88 0.00 0.95 0.99 0.96 0.99
duct epithelial cell 400 0.69 0.52 0.84 0.43 0.00 0.47 0.83 0.80 0.87
mesenchymal stem cell of adipose tissue 378 0.17 0.01 0.65 0.36 0.00 0.06 0.31 0.35 0.54
basal cell of prostate epithelium 336 0.72 0.09 0.87 0.46 0.00 0.37 0.84 0.76 0.83
endothelial cell of artery 369 0.43 0.42 0.75 0.48 0.00 0.52 0.66 0.55 0.73
stromal cell 362 0.43 0.05 0.44 0.44 0.00 0.38 0.76 0.71 0.82
thymic fibroblast type 1 322 0.00 0.01 0.85 0.19 0.00 0.00 0.53 0.50 0.31
pulmonary alveolar type 1 cell 313 0.97 0.93 0.96 0.79 0.00 0.92 0.98 0.93 0.98
spermatocyte 317 0.84 0.00 0.94 0.57 0.00 0.84 0.98 0.94 0.97
pancreatic ductal cell 267 0.89 0.39 0.92 0.64 0.00 0.11 0.97 0.90 0.96
regulatory T cell 261 0.08 0.00 0.24 0.04 0.00 0.21 0.17 0.18 0.32
ventricular cardiac muscle cell 249 0.21 0.18 0.70 0.25 0.00 0.26 0.77 0.79 0.71
endothelial cell of lymphatic vessel 256 0.63 0.57 0.85 0.56 0.00 0.52 0.61 0.57 0.68
hematopoietic precursor cell 217 0.61 0.69 0.78 0.72 0.00 0.52 0.63 0.62 0.80
retinal blood vessel endothelial cell 188 0.03 0.00 0.79 0.16 0.00 0.00 0.65 0.50 0.59
small intestine goblet cell 210 0.81 0.63 0.87 0.51 0.00 0.64 0.93 0.85 0.93
gamma-delta T cell 214 0.00 0.10 0.62 0.19 0.00 0.52 0.69 0.54 0.66
fibroblast of cardiac tissue 196 0.94 0.45 0.97 0.06 0.00 0.32 0.83 0.65 0.95
paneth cell of epithelium of small intestine 191 0.56 0.48 0.65 0.20 0.00 0.21 0.69 0.65 0.77
club cell 184 0.71 0.74 0.83 0.53 0.00 0.72 0.79 0.75 0.88
intestinal crypt stem cell of colon 165 0.63 0.64 0.55 0.29 0.00 0.06 0.79 0.79 0.81
progenitor cell of mammary luminal epithelium 169 0.99 0.00 0.99 0.97 0.00 0.97 0.96 0.91 0.99
epithelial cell 167 0.84 0.46 0.93 0.23 0.00 0.46 0.91 0.90 0.94
basophil 166 0.00 0.18 0.95 0.46 0.00 0.62 0.75 0.71 0.84
large intestine goblet cell 173 0.86 0.64 0.82 0.49 0.00 0.54 0.94 0.85 0.93
eye photoreceptor cell 150 0.90 0.91 0.93 0.95 0.00 0.88 0.96 0.97 0.96
epithelial cell of uterus 147 0.85 0.39 0.91 0.31 0.00 0.36 0.84 0.87 0.95
enterocyte of epithelium proper of small intestine 135 0.30 0.01 0.55 0.16 0.00 0.10 0.56 0.55 0.66
tissue-resident macrophage 149 0.48 0.00 0.80 0.24 0.00 0.22 0.45 0.51 0.72
acinar cell 127 0.83 0.67 0.87 0.72 0.00 0.44 0.92 0.83 0.94
non-classical monocyte 129 0.00 0.38 0.34 0.09 0.00 0.25 0.27 0.30 0.46
lung ciliated cell 113 0.62 0.53 0.97 0.66 0.00 0.79 0.91 0.91 0.91
activated CD8-positive, alpha-beta T cell 128 0.26 0.00 0.75 0.01 0.00 0.04 0.33 0.31 0.43
alveolar adventitial fibroblast 102 0.43 0.07 0.86 0.37 0.00 0.37 0.75 0.69 0.87
naive thymus-derived CD8-positive, alpha-beta T cell 124 0.15 0.00 0.38 0.07 0.00 0.14 0.17 0.13 0.34
adventitial cell 105 0.24 0.00 0.69 0.25 0.00 0.08 0.25 0.31 0.63
respiratory goblet cell 108 0.18 0.55 0.84 0.47 0.00 0.29 0.60 0.64 0.77
theca cell 125 0.00 0.03 0.82 0.52 0.00 0.64 0.78 0.60 0.82
myeloid leukocyte 107 0.15 0.00 0.64 0.11 0.00 0.09 0.18 0.16 0.46
keratocyte 87 0.00 0.00 0.50 0.08 0.00 0.20 0.37 0.31 0.31
enteroglial cell 105 0.54 0.80 0.96 0.73 0.00 0.84 0.94 0.78 0.89
erythroid progenitor cell 92 0.58 0.58 0.68 0.60 0.00 0.58 0.65 0.65 0.70
innate lymphoid cell 99 0.21 0.19 0.33 0.32 0.00 0.28 0.18 0.23 0.40
myometrial cell 99 0.48 0.00 0.83 0.48 0.00 0.39 0.62 0.65 0.84
endothelial cell of vascular tree 82 0.27 0.07 0.58 0.48 0.00 0.40 0.55 0.41 0.61
hematopoietic stem cell 89 0.61 0.62 0.69 0.71 0.00 0.69 0.76 0.70 0.79
salivary gland cell 84 0.00 0.00 0.85 0.49 0.00 0.36 0.65 0.58 0.85
granulocyte 74 0.20 0.00 0.56 0.35 0.00 0.17 0.25 0.20 0.58
CD8-positive, alpha-beta thymocyte 66 0.15 0.00 0.29 0.22 0.00 0.43 0.27 0.20 0.44
ciliated columnar cell of tracheobronchial tree 86 0.00 0.08 0.94 0.64 0.00 0.62 0.93 0.91 0.92
intrahepatic cholangiocyte 68 0.97 0.11 0.94 0.30 0.00 0.39 0.99 0.83 0.96
mural cell 68 0.31 0.23 0.92 0.14 0.00 0.32 0.61 0.48 0.69
intestinal crypt stem cell of small intestine 67 0.00 0.23 0.12 0.04 0.00 0.12 0.31 0.37 0.40
activated CD4-positive, alpha-beta T cell 61 0.05 0.00 0.28 0.06 0.00 0.15 0.10 0.10 0.19
myeloid dendritic cell 56 0.12 0.15 0.29 0.23 0.00 0.14 0.11 0.14 0.24
Mueller cell 44 0.53 0.51 0.61 0.67 0.00 0.17 0.83 0.89 0.86
fast muscle cell 40 0.42 0.42 0.88 0.61 0.00 0.72 0.77 0.76 0.86
platelet 45 0.89 0.86 0.90 0.94 0.00 0.63 0.88 0.69 0.89
myoepithelial cell 43 0.35 0.36 0.81 0.42 0.00 0.50 0.61 0.41 0.76
common myeloid progenitor 44 0.00 0.56 0.68 0.38 0.00 0.49 0.68 0.55 0.76
thymocyte 59 0.00 0.00 0.39 0.25 0.00 0.34 0.32 0.27 0.70
intestinal tuft cell 45 0.87 0.90 0.98 0.82 0.00 0.58 0.96 0.92 0.94
pancreatic stellate cell 44 0.00 0.00 0.93 0.33 0.00 0.03 0.60 0.40 0.68
tendon cell 32 0.00 0.06 0.40 0.24 0.00 0.12 0.42 0.23 0.48
muscle cell 47 0.51 0.00 0.93 0.84 0.00 0.78 0.76 0.83 0.93
microglial cell 40 0.11 0.00 0.59 0.08 0.00 0.05 0.25 0.13 0.32
enterocyte of epithelium proper of jejunum 46 0.00 0.00 0.10 0.16 0.00 0.03 0.58 0.41 0.60
mesothelial cell 33 0.53 0.60 0.85 0.65 0.00 0.45 0.64 0.60 0.70
colon endothelial cell 30 0.00 0.00 0.76 0.05 0.00 0.05 0.28 0.16 0.32
colon macrophage 30 0.00 0.00 0.63 0.00 0.00 0.04 0.20 0.19 0.17
serous cell of epithelium of trachea 25 0.00 0.00 0.78 0.36 0.00 0.20 0.42 0.49 0.83
ciliated epithelial cell 35 0.00 0.00 0.90 0.46 0.00 0.53 0.99 0.88 0.93
Schwann cell 36 0.00 0.46 0.87 0.32 0.00 0.34 0.77 0.70 0.85
supporting cell of vestibular epithelium 31 0.86 0.00 0.45 0.64 0.00 0.49 1.00 0.85 0.94
mucus secreting cell 30 0.00 0.07 0.91 0.35 0.00 0.35 0.67 0.62 0.87
enteroendocrine cell of small intestine 32 0.66 0.16 0.73 0.33 0.00 0.36 0.85 0.76 0.88
ovarian surface epithelial cell 19 0.00 0.47 0.82 0.16 0.00 0.27 0.84 0.67 0.83
transit amplifying cell of colon 22 0.00 0.30 0.39 0.06 0.00 0.08 0.60 0.38 0.56
glandular epithelial cell 25 0.00 0.14 0.65 0.18 0.00 0.33 0.94 0.62 0.81
melanocyte 19 0.00 0.32 0.59 0.12 0.00 0.21 0.68 0.73 0.84
tracheal goblet cell 32 0.00 0.37 0.64 0.57 0.00 0.30 0.78 0.54 0.74
hepatic stellate cell 16 0.56 0.00 0.69 0.00 0.00 0.03 0.50 0.35 0.67
bronchial smooth muscle cell 14 0.00 0.00 0.48 0.14 0.00 0.11 0.17 0.16 0.44
paneth cell of colon 24 0.00 0.27 0.45 0.47 0.00 0.15 0.68 0.32 0.81
tongue muscle cell 24 0.00 0.00 0.78 0.15 0.00 0.14 0.60 0.34 0.83
leukocyte 21 0.00 0.00 0.02 0.08 0.00 0.07 0.06 0.10 0.10
tuft cell of colon 16 0.00 0.10 0.64 0.19 0.00 0.47 0.86 0.63 0.83
slow muscle cell 17 0.00 0.26 0.82 0.25 0.00 0.55 0.77 0.68 0.91
ionocyte 12 0.00 0.28 0.80 0.38 0.00 0.41 0.85 0.56 0.91
connective tissue cell 21 0.00 0.00 0.95 0.00 0.00 0.13 0.48 0.25 0.76
neuro-medullary thymic epithelial cell 9 0.27 0.41 0.89 0.20 0.00 0.29 0.34 0.39 0.38
sebum secreting cell 10 0.00 0.01 0.75 0.33 0.00 0.04 0.78 0.49 0.90
endothelial cell of arteriole 17 0.00 0.00 0.81 0.00 0.00 0.00 0.52 0.25 0.64
male germ cell 9 0.00 0.00 0.94 0.00 0.00 0.34 0.95 0.73 0.94
type B pancreatic cell 9 0.00 0.20 0.95 0.74 0.00 0.39 1.00 0.89 1.00
hematopoietic cell 9 0.00 0.00 0.20 0.17 0.00 0.16 0.48 0.50 0.46
plasmacytoid dendritic cell 14 0.00 0.67 0.64 0.45 0.00 0.16 0.58 0.38 0.73
neuron 6 0.00 0.00 0.91 0.25 0.00 0.20 0.52 0.53 0.92
myeloid cell 6 0.00 0.00 0.00 0.00 0.00 0.00 0.32 0.11 0.40
myo-medullary thymic epithelial cell 10 0.00 0.00 0.95 0.67 0.00 0.43 0.82 0.67 0.67
Langerhans cell 4 0.00 0.40 1.00 0.22 0.00 0.07 0.18 0.20 0.67
interstitial cell of Cajal 6 0.00 0.00 1.00 0.00 0.00 0.19 0.27 0.43 1.00
retinal pigment epithelial cell 6 0.00 0.60 0.80 0.67 0.00 0.75 0.92 0.92 1.00
peritubular myoid cell 10 0.36 0.00 0.43 0.00 0.00 0.43 0.67 0.44 0.63
spermatogonium 7 0.00 0.00 0.44 0.00 0.00 0.24 0.86 0.67 0.73
retinal bipolar neuron 2 0.00 0.00 0.67 0.40 0.00 0.29 0.67 1.00 1.00
endothelial cell of venule 7 0.00 0.00 0.73 0.00 0.00 0.00 0.71 0.33 0.25
vestibular dark cell 5 0.00 0.00 0.00 0.00 0.00 0.04 0.89 0.67 0.00
pancreatic A cell 2 0.00 0.00 0.80 0.00 0.00 0.00 1.00 0.67 1.00
type L enteroendocrine cell 3 0.00 0.00 0.40 0.00 0.00 0.38 1.00 0.44 1.00
medullary thymic epithelial cell 3 0.00 0.00 0.80 0.00 0.00 0.03 0.86 0.40 1.00
adipocyte 4 0.00 0.00 0.29 0.00 0.00 0.00 0.46 0.00 0.40
transit amplifying cell of small intestine 2 0.00 0.00 0.00 0.00 0.00 0.00 0.33 0.00 0.00
taste receptor cell 4 0.00 0.00 0.67 0.00 0.00 0.27 0.33 0.09 0.67
enterochromaffin-like cell 1 0.00 0.00 0.00 0.00 0.00 0.40 1.00 0.40 1.00
enteroendocrine cell 4 0.00 0.00 1.00 0.44 0.00 0.31 0.67 0.50 0.75
pulmonary ionocyte 1 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.67 0.00
glial cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.25 0.00 0.00
oocyte 2 0.00 0.02 1.00 1.00 0.00 0.15 1.00 1.00 1.00
serous cell of epithelium of bronchus 2 0.00 0.00 0.67 0.40 0.00 0.09 0.67 0.67 0.67
radial glial cell 3 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.25 0.00
Leydig cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.67 0.33 0.00
pancreatic D cell 1 0.00 0.00 1.00 0.00 0.00 0.00 1.00 1.00 1.00
T follicular helper cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
retina horizontal cell 1 0.00 0.00 0.00 0.00 0.00 0.03 0.00 0.00 0.00
erythroid lineage cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
pancreatic PP cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
epithelial fate stem cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
mesenchymal cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

The train accuracies are computed on the training data.

Cell Type N cells celltypist knn bbknn knn harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
B cell 103041 0.99 0.99 0.99 0.99 0.00 0.97 0.98 0.98 0.99
CD4-positive, alpha-beta T cell 87356 0.57 0.78 0.87 0.82 0.00 0.57 0.43 0.49 0.82
fibroblast 74984 0.78 0.75 0.97 0.84 0.00 0.85 0.66 0.65 0.93
CD8-positive, alpha-beta T cell 68662 0.72 0.77 0.87 0.82 0.00 0.75 0.57 0.63 0.83
neutrophil 62691 0.95 0.97 0.99 0.98 0.00 0.95 0.95 0.94 0.99
macrophage 62114 0.79 0.83 0.95 0.87 0.00 0.78 0.73 0.71 0.91
stromal cell of ovary 31562 0.94 0.70 0.94 0.84 0.00 0.95 0.96 0.93 0.98
endothelial cell 30425 0.69 0.70 0.96 0.82 0.00 0.77 0.72 0.66 0.91
basal cell 30188 0.85 0.80 0.94 0.82 0.00 0.83 0.87 0.83 0.94
plasma cell 24698 0.97 0.98 0.98 0.97 0.00 0.97 0.98 0.97 0.99
bladder urothelial cell 24521 0.97 0.96 0.98 0.76 0.00 0.92 0.98 0.97 0.99
monocyte 23187 0.45 0.30 0.86 0.72 0.00 0.56 0.51 0.56 0.72
mesenchymal stem cell 21176 0.84 0.74 0.95 0.68 0.00 0.93 0.90 0.81 0.95
smooth muscle cell 16656 0.68 0.64 0.93 0.85 0.00 0.85 0.75 0.75 0.88
classical monocyte 16363 0.52 0.56 0.84 0.73 0.00 0.71 0.59 0.67 0.78
luminal epithelial cell of mammary gland 13840 0.98 0.00 0.98 0.83 0.00 0.94 0.98 0.97 0.99
capillary endothelial cell 13764 0.68 0.57 0.93 0.80 0.00 0.78 0.71 0.68 0.84
erythrocyte 13116 0.97 0.96 0.98 0.98 0.00 0.97 0.96 0.96 0.98
natural killer cell 12793 0.73 0.74 0.83 0.80 0.00 0.74 0.70 0.70 0.77
enterocyte of epithelium proper of duodenum 12093 0.90 0.00 0.87 0.71 0.00 0.94 0.92 0.88 0.97
stratified squamous epithelial cell 11064 0.82 0.71 0.93 0.81 0.00 0.86 0.85 0.82 0.90
acinar cell of salivary gland 11001 0.88 0.71 0.97 0.78 0.00 0.93 0.94 0.91 0.98
pulmonary alveolar type 2 cell 10410 0.94 0.96 0.99 0.87 0.00 0.95 0.97 0.96 0.98
conjunctival epithelial cell 9930 0.92 0.70 0.91 0.73 0.00 0.94 0.94 0.87 0.96
pericyte 9818 0.57 0.50 0.90 0.76 0.00 0.72 0.62 0.68 0.82
luminal cell of prostate epithelium 9588 0.90 0.44 0.96 0.81 0.00 0.93 0.94 0.92 0.96
cardiac endothelial cell 9044 0.94 0.78 0.98 0.82 0.00 0.96 0.95 0.89 0.97
naive thymus-derived CD4-positive, alpha-beta T cell 8845 0.23 0.02 0.51 0.28 0.00 0.28 0.24 0.30 0.37
kidney epithelial cell 8393 0.97 0.17 0.97 0.82 0.00 0.98 0.99 0.98 0.99
hepatocyte 6719 0.99 0.98 0.98 0.87 0.00 0.98 0.99 0.97 1.00
blood vessel smooth muscle cell 5977 0.68 0.20 0.95 0.88 0.00 0.93 0.89 0.80 0.95
enterocyte of epithelium proper of ileum 5829 0.94 0.00 0.84 0.65 0.00 0.96 0.98 0.93 0.98
T cell 5617 0.40 0.17 0.70 0.41 0.00 0.39 0.34 0.39 0.62
mast cell 5620 0.85 0.84 0.97 0.93 0.00 0.93 0.91 0.90 0.96
skeletal muscle satellite stem cell 5591 0.87 0.93 0.98 0.91 0.00 0.96 0.94 0.91 0.97
regular atrial cardiac myocyte 5252 0.83 0.21 0.91 0.75 0.00 0.96 0.88 0.92 0.95
pancreatic acinar cell 4946 0.95 0.02 0.97 0.83 0.00 0.93 0.98 0.96 0.99
intermediate monocyte 4924 0.29 0.11 0.70 0.53 0.00 0.28 0.37 0.46 0.59
mature NK T cell 4847 0.42 0.40 0.69 0.56 0.00 0.51 0.40 0.48 0.64
mononuclear phagocyte 4793 0.43 0.00 0.96 0.54 0.00 0.81 0.67 0.52 0.92
fibroblast of breast 4738 0.95 0.00 0.99 0.74 0.00 0.85 0.87 0.67 0.98
vascular associated smooth muscle cell 4493 0.65 0.01 0.86 0.67 0.00 0.70 0.63 0.65 0.79
vein endothelial cell 4211 0.35 0.07 0.87 0.63 0.00 0.56 0.51 0.49 0.72
CD4-positive, alpha-beta thymocyte 4182 0.37 0.00 0.74 0.48 0.00 0.57 0.43 0.39 0.70
enterocyte of epithelium of large intestine 4130 0.71 0.23 0.75 0.61 0.00 0.85 0.82 0.85 0.85
myofibroblast cell 4008 0.51 0.13 0.91 0.72 0.00 0.73 0.64 0.58 0.85
thymic fibroblast type 2 3771 0.52 0.00 0.86 0.56 0.00 0.88 0.67 0.55 0.90
corneal epithelial cell 3782 0.93 0.00 0.95 0.85 0.00 0.94 0.95 0.93 0.96
spermatid 3593 0.91 0.00 0.99 0.97 0.00 0.98 0.99 0.97 0.99
duct epithelial cell 3489 0.67 0.34 0.92 0.71 0.00 0.78 0.83 0.80 0.91
mesenchymal stem cell of adipose tissue 3399 0.18 0.00 0.75 0.54 0.00 0.50 0.34 0.37 0.58
basal cell of prostate epithelium 3159 0.71 0.01 0.93 0.74 0.00 0.85 0.84 0.78 0.89
endothelial cell of artery 3101 0.42 0.28 0.85 0.65 0.00 0.65 0.64 0.54 0.78
stromal cell 3095 0.43 0.00 0.69 0.57 0.00 0.80 0.77 0.73 0.92
thymic fibroblast type 1 2948 0.00 0.00 0.92 0.44 0.00 0.87 0.56 0.51 0.87
pulmonary alveolar type 1 cell 2803 0.97 0.89 0.99 0.94 0.00 0.95 0.98 0.95 0.98
spermatocyte 2753 0.83 0.00 0.97 0.92 0.00 0.94 0.98 0.96 0.98
pancreatic ductal cell 2452 0.89 0.07 0.95 0.82 0.00 0.93 0.96 0.92 0.97
regulatory T cell 2388 0.08 0.00 0.39 0.24 0.00 0.26 0.19 0.21 0.45
ventricular cardiac muscle cell 2350 0.26 0.00 0.81 0.66 0.00 0.96 0.79 0.85 0.88
endothelial cell of lymphatic vessel 2182 0.65 0.48 0.95 0.74 0.00 0.65 0.65 0.64 0.78
hematopoietic precursor cell 1923 0.57 0.64 0.83 0.79 0.00 0.50 0.64 0.62 0.83
retinal blood vessel endothelial cell 1901 0.05 0.00 0.92 0.48 0.00 0.95 0.69 0.55 0.90
small intestine goblet cell 1834 0.83 0.49 0.93 0.82 0.00 0.85 0.94 0.89 0.93
gamma-delta T cell 1763 0.00 0.07 0.78 0.42 0.00 0.58 0.68 0.51 0.82
fibroblast of cardiac tissue 1751 0.95 0.18 0.98 0.54 0.00 0.83 0.81 0.66 0.98
paneth cell of epithelium of small intestine 1662 0.56 0.32 0.79 0.60 0.00 0.65 0.72 0.70 0.83
club cell 1563 0.70 0.70 0.91 0.70 0.00 0.72 0.80 0.77 0.90
intestinal crypt stem cell of colon 1567 0.64 0.47 0.79 0.63 0.00 0.77 0.84 0.84 0.90
progenitor cell of mammary luminal epithelium 1525 0.98 0.00 0.99 0.97 0.00 0.94 0.97 0.94 0.99
epithelial cell 1506 0.82 0.13 0.98 0.72 0.00 0.90 0.93 0.91 0.95
basophil 1503 0.00 0.00 0.96 0.81 0.00 0.81 0.78 0.75 0.93
large intestine goblet cell 1384 0.86 0.14 0.93 0.76 0.00 0.82 0.93 0.88 0.94
eye photoreceptor cell 1380 0.90 0.91 0.96 0.95 0.00 0.71 0.98 0.97 0.97
epithelial cell of uterus 1270 0.87 0.18 0.98 0.69 0.00 0.89 0.85 0.87 0.98
enterocyte of epithelium proper of small intestine 1280 0.31 0.00 0.79 0.57 0.00 0.79 0.66 0.68 0.81
tissue-resident macrophage 1206 0.45 0.00 0.85 0.56 0.00 0.70 0.42 0.52 0.76
acinar cell 1218 0.89 0.31 0.97 0.86 0.00 0.89 0.93 0.89 0.96
non-classical monocyte 1155 0.00 0.32 0.56 0.41 0.00 0.24 0.32 0.36 0.60
lung ciliated cell 1096 0.68 0.19 0.98 0.90 0.00 0.97 0.96 0.92 0.98
activated CD8-positive, alpha-beta T cell 1019 0.28 0.00 0.86 0.40 0.00 0.57 0.34 0.32 0.71
alveolar adventitial fibroblast 1011 0.44 0.02 0.94 0.62 0.00 0.58 0.78 0.71 0.94
naive thymus-derived CD8-positive, alpha-beta T cell 932 0.13 0.00 0.59 0.31 0.00 0.30 0.17 0.15 0.55
adventitial cell 940 0.21 0.00 0.88 0.55 0.00 0.35 0.27 0.34 0.71
respiratory goblet cell 932 0.17 0.38 0.90 0.69 0.00 0.62 0.62 0.67 0.84
theca cell 913 0.00 0.00 0.88 0.76 0.00 0.48 0.72 0.57 0.88
myeloid leukocyte 895 0.19 0.00 0.85 0.42 0.00 0.68 0.22 0.23 0.77
keratocyte 914 0.00 0.00 0.78 0.28 0.00 0.52 0.40 0.37 0.80
enteroglial cell 885 0.51 0.58 0.97 0.87 0.00 0.76 0.94 0.81 0.89
erythroid progenitor cell 879 0.60 0.54 0.82 0.80 0.00 0.76 0.74 0.73 0.80
innate lymphoid cell 867 0.21 0.10 0.56 0.44 0.00 0.59 0.22 0.26 0.49
myometrial cell 818 0.44 0.00 0.87 0.78 0.00 0.70 0.66 0.67 0.84
endothelial cell of vascular tree 793 0.32 0.01 0.82 0.59 0.00 0.69 0.61 0.49 0.73
hematopoietic stem cell 769 0.61 0.59 0.86 0.82 0.00 0.74 0.87 0.84 0.88
salivary gland cell 766 0.00 0.00 0.93 0.80 0.00 0.75 0.70 0.64 0.93
granulocyte 695 0.20 0.00 0.69 0.65 0.00 0.35 0.29 0.24 0.69
CD8-positive, alpha-beta thymocyte 665 0.17 0.00 0.58 0.44 0.00 0.54 0.44 0.32 0.72
ciliated columnar cell of tracheobronchial tree 626 0.00 0.01 0.97 0.83 0.00 0.88 0.95 0.90 0.98
intrahepatic cholangiocyte 597 0.96 0.07 0.97 0.83 0.00 0.97 0.98 0.87 0.98
mural cell 550 0.28 0.12 0.96 0.66 0.00 0.71 0.66 0.53 0.96
intestinal crypt stem cell of small intestine 520 0.00 0.21 0.46 0.29 0.00 0.36 0.47 0.54 0.64
activated CD4-positive, alpha-beta T cell 511 0.03 0.00 0.56 0.30 0.00 0.26 0.14 0.14 0.35
myeloid dendritic cell 515 0.12 0.05 0.60 0.43 0.00 0.18 0.16 0.21 0.31
Mueller cell 462 0.52 0.44 0.83 0.79 0.00 0.49 0.92 0.92 0.91
fast muscle cell 455 0.32 0.47 0.94 0.85 0.00 0.88 0.81 0.88 0.92
platelet 449 0.90 0.89 0.96 0.96 0.00 0.68 0.91 0.75 0.95
myoepithelial cell 443 0.41 0.19 0.92 0.77 0.00 0.65 0.70 0.51 0.89
common myeloid progenitor 412 0.00 0.37 0.84 0.75 0.00 0.71 0.88 0.79 0.92
thymocyte 396 0.00 0.00 0.65 0.46 0.00 0.56 0.40 0.36 0.88
intestinal tuft cell 403 0.81 0.77 0.97 0.86 0.00 0.90 0.97 0.97 0.97
pancreatic stellate cell 392 0.00 0.00 0.96 0.59 0.00 0.56 0.68 0.42 0.92
tendon cell 388 0.00 0.02 0.74 0.18 0.00 0.35 0.49 0.31 0.81
muscle cell 359 0.50 0.00 0.98 0.94 0.00 0.95 0.79 0.93 0.95
microglial cell 366 0.09 0.01 0.78 0.27 0.00 0.36 0.38 0.20 0.56
enterocyte of epithelium proper of jejunum 359 0.00 0.00 0.60 0.47 0.00 0.73 0.63 0.44 0.95
mesothelial cell 317 0.56 0.42 0.94 0.89 0.00 0.81 0.73 0.72 0.81
colon endothelial cell 318 0.00 0.00 0.88 0.38 0.00 0.65 0.45 0.31 0.95
colon macrophage 298 0.00 0.00 0.86 0.43 0.00 0.49 0.29 0.30 0.92
serous cell of epithelium of trachea 301 0.00 0.00 0.87 0.67 0.00 0.35 0.58 0.60 0.94
ciliated epithelial cell 285 0.00 0.00 0.97 0.83 0.00 0.84 0.99 0.92 0.99
Schwann cell 282 0.00 0.31 0.87 0.71 0.00 0.70 0.88 0.78 0.89
supporting cell of vestibular epithelium 239 0.85 0.00 0.72 0.78 0.00 0.86 1.00 0.87 0.99
mucus secreting cell 240 0.00 0.01 0.86 0.69 0.00 0.64 0.71 0.77 0.92
enteroendocrine cell of small intestine 232 0.51 0.07 0.88 0.76 0.00 0.53 0.88 0.84 0.92
ovarian surface epithelial cell 222 0.00 0.11 0.92 0.83 0.00 0.86 0.90 0.70 0.94
transit amplifying cell of colon 215 0.00 0.26 0.65 0.49 0.00 0.47 0.78 0.61 0.88
glandular epithelial cell 210 0.00 0.03 0.89 0.67 0.00 0.58 0.88 0.72 0.98
melanocyte 215 0.00 0.14 0.86 0.61 0.00 0.79 0.77 0.81 0.93
tracheal goblet cell 200 0.00 0.10 0.86 0.76 0.00 0.55 0.78 0.61 0.96
hepatic stellate cell 207 0.52 0.00 0.83 0.42 0.00 0.48 0.60 0.44 0.77
bronchial smooth muscle cell 206 0.00 0.00 0.78 0.50 0.00 0.45 0.46 0.46 0.78
paneth cell of colon 193 0.00 0.07 0.77 0.60 0.00 0.41 0.76 0.34 0.90
tongue muscle cell 178 0.00 0.00 0.89 0.54 0.00 0.55 0.80 0.42 0.94
leukocyte 180 0.00 0.00 0.62 0.09 0.00 0.39 0.28 0.19 0.71
tuft cell of colon 162 0.00 0.06 0.89 0.58 0.00 0.84 0.94 0.92 0.98
slow muscle cell 157 0.00 0.12 0.88 0.74 0.00 0.75 0.88 0.91 0.96
ionocyte 148 0.00 0.10 0.80 0.62 0.00 0.51 0.83 0.76 0.93
connective tissue cell 131 0.00 0.00 0.97 0.83 0.00 0.28 0.49 0.28 0.98
neuro-medullary thymic epithelial cell 126 0.28 0.22 0.87 0.75 0.00 0.36 0.46 0.55 0.46
sebum secreting cell 125 0.00 0.02 0.92 0.25 0.00 0.65 0.86 0.67 0.93
endothelial cell of arteriole 115 0.00 0.00 0.95 0.36 0.00 0.20 0.74 0.44 0.97
male germ cell 107 0.00 0.00 0.91 0.81 0.00 0.51 1.00 0.80 1.00
type B pancreatic cell 93 0.00 0.00 0.93 0.86 0.00 0.65 1.00 0.94 1.00
hematopoietic cell 91 0.00 0.00 0.81 0.63 0.00 0.26 0.61 0.49 0.80
plasmacytoid dendritic cell 85 0.00 0.31 0.69 0.67 0.00 0.15 0.63 0.51 0.73
neuron 76 0.00 0.00 0.97 0.76 0.00 0.58 0.61 0.79 0.92
myeloid cell 75 0.00 0.00 0.58 0.03 0.00 0.49 0.41 0.27 0.87
myo-medullary thymic epithelial cell 67 0.00 0.00 0.96 0.85 0.00 0.91 0.81 0.93 0.99
Langerhans cell 72 0.00 0.10 0.83 0.57 0.00 0.11 0.34 0.44 0.82
interstitial cell of Cajal 65 0.00 0.00 0.93 0.57 0.00 0.56 0.26 0.49 0.94
retinal pigment epithelial cell 61 0.00 0.00 0.96 0.90 0.00 0.90 1.00 0.94 0.99
peritubular myoid cell 57 0.18 0.00 0.78 0.50 0.00 0.30 0.67 0.43 0.77
spermatogonium 57 0.00 0.00 0.69 0.58 0.00 0.44 0.93 0.78 0.90
retinal bipolar neuron 59 0.00 0.08 0.85 0.69 0.00 0.70 0.83 0.91 0.93
endothelial cell of venule 45 0.00 0.00 0.93 0.27 0.00 0.22 0.87 0.62 0.96
vestibular dark cell 44 0.00 0.00 0.54 0.23 0.00 0.71 0.99 0.85 0.98
pancreatic A cell 46 0.00 0.00 0.90 0.88 0.00 0.65 1.00 1.00 1.00
type L enteroendocrine cell 41 0.00 0.05 0.89 0.56 0.00 0.86 0.96 0.94 0.97
medullary thymic epithelial cell 40 0.00 0.00 0.62 0.29 0.00 0.44 0.93 0.76 0.91
adipocyte 34 0.00 0.00 0.73 0.41 0.00 0.44 0.60 0.67 0.84
transit amplifying cell of small intestine 32 0.00 0.00 0.41 0.48 0.00 0.16 0.82 0.74 0.89
taste receptor cell 28 0.00 0.00 0.86 0.64 0.00 0.38 0.85 0.33 0.95
enterochromaffin-like cell 26 0.00 0.03 0.88 0.63 0.00 0.71 0.96 0.90 0.96
enteroendocrine cell 21 0.00 0.00 0.93 0.59 0.00 0.51 0.91 0.88 0.95
pulmonary ionocyte 24 0.00 0.00 0.73 0.59 0.00 0.35 1.00 0.91 0.98
glial cell 19 0.00 0.00 0.71 0.41 0.00 0.29 0.46 0.33 0.78
oocyte 16 0.00 0.00 0.91 0.79 0.00 0.17 0.89 0.91 0.91
serous cell of epithelium of bronchus 13 0.00 0.00 0.83 0.35 0.00 0.23 0.84 0.87 1.00
radial glial cell 10 0.00 0.00 0.00 0.00 0.00 0.11 0.22 0.31 0.38
Leydig cell 9 0.00 0.00 0.31 0.29 0.00 0.07 0.82 0.31 0.82
pancreatic D cell 8 0.00 0.00 0.55 0.86 0.00 0.25 1.00 0.89 1.00
T follicular helper cell 6 0.00 0.00 0.00 0.00 0.00 0.02 0.86 0.32 0.55
retina horizontal cell 4 0.00 0.00 0.00 0.00 0.00 0.05 1.00 1.00 0.57
erythroid lineage cell 2 0.00 0.00 0.00 0.00 0.00 0.33 1.00 0.67 0.00
pancreatic PP cell 1 0.00 0.00 0.00 0.00 0.00 0.67 1.00 1.00 1.00
epithelial fate stem cell 2 0.00 0.00 0.00 0.00 0.00 0.01 1.00 1.00 0.00
mesenchymal cell 2 0.00 0.00 0.00 0.00 0.00 0.01 0.22 0.31 0.00

References

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues, The Tabula Sapiens Consortium; bioRxiv, doi: https://doi.org/10.1101/2024.12.03.626516

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