Single cell type - TPM3 - The Human Protein Atlas

TPM3

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GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	TPM3
Gene descriptionⁱ Full gene name according to HGNC.	Tropomyosin 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes Plasma proteins
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	11

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Non-specific - Mixed function (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Monocytes)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.31
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Low cell type specificity
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types RNA single cell type specificity: Cell type enhanced (Monocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

TPM3 is part of cluster 45 Non-specific - Mixed function with confidenceⁱ 1
349 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TMSB10	Thymosin beta 10	0.5669	45
ARPC1B	Actin related protein 2/3 complex subunit 1B	0.5528	57
LRRFIP1	LRR binding FLII interacting protein 1	0.5431	29
CFL1	Cofilin 1	0.5420	45
ACTB	Actin beta	0.5369	14
ARHGDIA	Rho GDP dissociation inhibitor alpha	0.5339	45
CDC42	Cell division cycle 42	0.5318	45
SH3BGRL3	SH3 domain binding glutamate rich protein like 3	0.5293	45
TAGLN2	Transgelin 2	0.5227	57
DIAPH1	Diaphanous related formin 1	0.5144	45
ARPC4	Actin related protein 2/3 complex subunit 4	0.5059	14
YWHAB	Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta	0.4976	45
TP53BP2	Tumor protein p53 binding protein 2	0.4775	29
SRGN	Serglycin	0.4761	29
MOB1A	MOB kinase activator 1A	0.4755	14

IMMUNE CELLS

TPM3 is part of cluster 29 Non-specific - Unknown function with confidenceⁱ 0.66
401 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data.	Clusterⁱ ID of the expression cluster of the neighboring gene.
CLEC12A	C-type lectin domain family 12 member A	1.0000	29
PRKCD	Protein kinase C delta	1.0000	29
EFTUD2	Elongation factor Tu GTP binding domain containing 2	1.0000	29
MTFR1L	Mitochondrial fission regulator 1 like	0.9762	29
ARRDC1	Arrestin domain containing 1	0.9762	25
YIF1B	Yip1 interacting factor homolog B, membrane trafficking protein	0.9762	29
ZNG1B	Zn regulated GTPase metalloprotein activator 1B	0.9762	29
CD101	CD101 molecule	0.9762	25
SLX1A	SLX1 homolog A, structure-specific endonuclease subunit	0.9762	25
SERPINB6	Serpin family B member 6	0.9762	29
ENY2	ENY2 transcription and export complex 2 subunit	0.9762	29
ADPRS	ADP-ribosylserine hydrolase	0.9762	29
TPI1	Triosephosphate isomerase 1	0.9762	29
MICU1	Mitochondrial calcium uptake 1	0.9762	29
BABAM1	BRISC and BRCA1 A complex member 1	0.9762	29

Adipocytes	359.3 nTPM
Adipose tissue	431.2 nTPM
Breast	287.4 nTPM

Alveolar cells type 1	404.0 nTPM
Lung	404.0 nTPM

Alveolar cells type 2	237.4 nTPM
Lung	237.4 nTPM

Astrocytes	16.7 nTPM
Brain	16.7 nTPM

B-cells	333.4 nTPM
Skin	538.7 nTPM
Adipose tissue	489.3 nTPM
Salivary gland	368.1 nTPM
Lymph node	357.0 nTPM
Esophagus	342.2 nTPM
Spleen	329.1 nTPM
Stomach	324.4 nTPM
Thymus	321.8 nTPM
Bone marrow	302.5 nTPM
Lung	276.3 nTPM
Kidney	260.0 nTPM
PBMC	237.1 nTPM
Liver	188.4 nTPM

Basal squamous epithelial cells	148.7 nTPM
Esophagus	148.7 nTPM

Ciliated cells	198.8 nTPM
Endometrium	365.5 nTPM
Fallopian tube	218.2 nTPM
Lung	124.3 nTPM
Bronchus	87.0 nTPM

Club cells	144.3 nTPM
Prostate	167.0 nTPM
Lung	152.0 nTPM
Bronchus	113.9 nTPM

Dendritic cells	392.2 nTPM
Adipose tissue	453.5 nTPM
PBMC	331.0 nTPM

Endothelial cells	392.1 nTPM
Fallopian tube	756.3 nTPM
Lung	600.7 nTPM
Salivary gland	517.1 nTPM
Skin	500.5 nTPM
Thymus	489.4 nTPM
Esophagus	485.0 nTPM
Vascular	459.8 nTPM
Endometrium	455.2 nTPM
Placenta	387.2 nTPM
Heart muscle	380.0 nTPM
Tongue	359.2 nTPM
Pancreas	341.3 nTPM
Skeletal muscle	295.3 nTPM
Breast	292.6 nTPM
Prostate	213.4 nTPM
Testis	192.9 nTPM
Ovary	187.1 nTPM
Liver	144.9 nTPM

Enteroendocrine cells	183.0 nTPM
Colon	354.5 nTPM
Rectum	115.7 nTPM
Small intestine	79.0 nTPM

Erythroid cells	173.6 nTPM
Bone marrow	305.3 nTPM
Liver	42.0 nTPM

Fibroblasts	155.3 nTPM
Pancreas	302.2 nTPM
Heart muscle	242.0 nTPM
Vascular	198.3 nTPM
Liver	187.4 nTPM
Lung	186.0 nTPM
Thymus	162.1 nTPM
Stomach	148.4 nTPM
Salivary gland	142.7 nTPM
Adipose tissue	142.5 nTPM
Placenta	131.1 nTPM
Skeletal muscle	122.0 nTPM
Skin	121.2 nTPM
Fallopian tube	114.9 nTPM
Breast	109.4 nTPM
Esophagus	108.3 nTPM
Prostate	66.7 nTPM

Granulocytes	345.8 nTPM
Fallopian tube	479.7 nTPM
Lung	324.7 nTPM
Tongue	232.8 nTPM

Intestinal goblet cells	245.0 nTPM
Colon	369.8 nTPM
Small intestine	192.5 nTPM
Rectum	172.8 nTPM

Bipolar cells	93.3 nTPM
Eye	93.3 nTPM

Cholangiocytes	133.5 nTPM
Liver	133.5 nTPM

Collecting duct cells	101.1 nTPM
Kidney	101.1 nTPM

Cone photoreceptor cells	49.3 nTPM
Eye	49.3 nTPM

Lymphatic endothelial cells	325.0 nTPM
Fallopian tube	519.1 nTPM
Ovary	130.9 nTPM

Macrophages	576.4 nTPM
Adipose tissue	912.6 nTPM
Stomach	872.0 nTPM
Fallopian tube	824.8 nTPM
Endometrium	733.0 nTPM
Skeletal muscle	698.4 nTPM
Thymus	648.1 nTPM
Vascular	614.6 nTPM
Bone marrow	597.9 nTPM
Esophagus	570.3 nTPM
Spleen	510.3 nTPM
Kidney	500.0 nTPM
Lung	486.1 nTPM
Breast	484.6 nTPM
Skin	458.0 nTPM
Tongue	450.6 nTPM
Pancreas	448.1 nTPM
Salivary gland	417.4 nTPM
Testis	378.2 nTPM
Prostate	346.9 nTPM

Paneth cells	334.7 nTPM
Colon	535.6 nTPM
Rectum	268.1 nTPM
Small intestine	200.3 nTPM

Plasma cells	215.5 nTPM
Fallopian tube	287.2 nTPM
Spleen	250.7 nTPM
Thymus	225.4 nTPM
Bone marrow	217.5 nTPM
Liver	204.8 nTPM
Esophagus	187.1 nTPM
Stomach	178.0 nTPM
Salivary gland	173.3 nTPM

Schwann cells	569.8 nTPM
Adipose tissue	1502.6 nTPM
Vascular	170.8 nTPM
Esophagus	35.9 nTPM

Serous glandular cells	135.3 nTPM
Salivary gland	146.9 nTPM
Tongue	123.7 nTPM

Smooth muscle cells	97.2 nTPM
Liver	221.6 nTPM
Endometrium	125.2 nTPM
Skeletal muscle	125.1 nTPM
Fallopian tube	118.7 nTPM
Tongue	110.5 nTPM
Placenta	108.5 nTPM
Salivary gland	97.5 nTPM
Esophagus	90.1 nTPM
Adipose tissue	83.7 nTPM
Thymus	77.5 nTPM
Prostate	76.6 nTPM
Vascular	74.4 nTPM
Breast	71.3 nTPM
Lung	69.4 nTPM
Skin	61.0 nTPM
Ovary	44.4 nTPM

Suprabasal keratinocytes	197.8 nTPM
Tongue	270.4 nTPM
Skin	125.3 nTPM

T-cells	399.4 nTPM
Adipose tissue	728.1 nTPM
Endometrium	555.1 nTPM
Stomach	538.8 nTPM
Esophagus	537.8 nTPM
Fallopian tube	507.7 nTPM
Bone marrow	438.8 nTPM
Skeletal muscle	426.1 nTPM
Spleen	402.8 nTPM
Skin	392.5 nTPM
Tongue	388.6 nTPM
Lymph node	359.2 nTPM
Breast	355.2 nTPM
Colon	351.0 nTPM
Kidney	337.8 nTPM
Lung	322.5 nTPM
Vascular	320.4 nTPM
PBMC	304.1 nTPM
Thymus	283.0 nTPM
Prostate	281.2 nTPM
Salivary gland	278.6 nTPM
Liver	278.3 nTPM

Undifferentiated cells	255.2 nTPM
Colon	352.7 nTPM
Small intestine	237.8 nTPM
Rectum	175.0 nTPM

Amygdala excitatory	69.0 nTPM
Cerebral cortex	76.6 nTPM
Hippocampus	75.0 nTPM
Amygdala	71.1 nTPM
Basal ganglia	65.7 nTPM
Hypothalamus	65.0 nTPM
Thalamus	60.8 nTPM

Astrocyte	24.9 nTPM
Cerebral cortex	29.7 nTPM
Amygdala	29.5 nTPM
Hippocampus	28.9 nTPM
Pons	25.6 nTPM
Medulla oblongata	24.5 nTPM
Hypothalamus	24.2 nTPM
Thalamus	23.8 nTPM
Basal ganglia	23.2 nTPM
Midbrain	22.3 nTPM
Cerebellum	21.5 nTPM
Spinal cord	20.4 nTPM

Bergmann glia	31.0 nTPM
Cerebellum	34.4 nTPM
Medulla oblongata	29.8 nTPM
Pons	28.8 nTPM

Central nervous system macrophage	111.3 nTPM
Pons	120.2 nTPM
Basal ganglia	117.3 nTPM
Midbrain	116.2 nTPM
Amygdala	116.1 nTPM
Thalamus	114.2 nTPM
Hypothalamus	111.7 nTPM
Cerebellum	111.6 nTPM
Medulla oblongata	108.6 nTPM
Hippocampus	107.6 nTPM
Cerebral cortex	104.5 nTPM
Spinal cord	96.3 nTPM

Cerebellar inhibitory	71.6 nTPM
Spinal cord	93.5 nTPM
Cerebellum	72.5 nTPM
Medulla oblongata	66.5 nTPM
Pons	66.4 nTPM
Midbrain	59.1 nTPM

Cge interneuron	64.9 nTPM
Cerebral cortex	70.9 nTPM
Hippocampus	67.4 nTPM
Thalamus	65.3 nTPM
Basal ganglia	63.3 nTPM
Midbrain	63.2 nTPM
Amygdala	62.0 nTPM
Hypothalamus	61.9 nTPM

Choroid plexus epithelial cell	25.2 nTPM
Medulla oblongata	31.6 nTPM
Basal ganglia	28.0 nTPM
Thalamus	27.4 nTPM
Hippocampus	13.9 nTPM

Committed oligodendrocyte precursor	28.8 nTPM
Medulla oblongata	38.7 nTPM
Thalamus	38.0 nTPM
Pons	33.6 nTPM
Cerebral cortex	32.9 nTPM
Basal ganglia	30.1 nTPM
Amygdala	28.8 nTPM
Midbrain	26.9 nTPM
Hypothalamus	26.6 nTPM
Cerebellum	22.2 nTPM
Hippocampus	21.0 nTPM
Spinal cord	18.4 nTPM

Deep-layer corticothalamic and 6b	80.6 nTPM
Midbrain	89.9 nTPM
Hippocampus	81.8 nTPM
Cerebral cortex	81.6 nTPM
Hypothalamus	78.3 nTPM
Amygdala	76.6 nTPM
Basal ganglia	75.4 nTPM

Deep-layer intratelencephalic	93.1 nTPM
Hippocampus	100.9 nTPM
Cerebral cortex	95.3 nTPM
Basal ganglia	94.8 nTPM
Hypothalamus	89.4 nTPM
Amygdala	84.9 nTPM