Single cell type - TOMM40 - The Human Protein Atlas

TOMM40

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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.	TOMM40
Gene descriptionⁱ Full gene name according to HGNC.	Translocase of outer mitochondrial membrane 40
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transporters
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.	6

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 - Basic cellular processes (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 (Extravillous trophoblasts)
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 (Extravillous trophoblasts)

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

TOMM40 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 1
835 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.
DOHH	Deoxyhypusine hydroxylase	0.7288	39
MRPL12	Mitochondrial ribosomal protein L12	0.7242	39
PUS1	Pseudouridine synthase 1	0.6946	39
ATAD3A	ATPase family AAA domain containing 3A	0.6819	39
POLD1	DNA polymerase delta 1, catalytic subunit	0.6817	52
MRPL11	Mitochondrial ribosomal protein L11	0.6610	39
C1QBP	Complement C1q binding protein	0.6189	39
RABL6	RAB, member RAS oncogene family like 6	0.6189	39
MRPL4	Mitochondrial ribosomal protein L4	0.6116	39
BOP1	BOP1 ribosomal biogenesis factor	0.6037	39
XRCC3	X-ray repair cross complementing 3	0.5973	52
ATAD3B	ATPase family AAA domain containing 3B	0.5898	39
MRPS12	Mitochondrial ribosomal protein S12	0.5894	39
EIF5A	Eukaryotic translation initiation factor 5A	0.5856	39
NOM1	Nucleolar protein with MIF4G domain 1	0.5827	39

IMMUNE CELLS

TOMM40 is part of cluster 45 Eosinophils - Unknown function with confidenceⁱ 0.49
257 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.
BRD9	Bromodomain containing 9	0.9762	45
SEC63	SEC63 homolog, protein translocation regulator	0.9762	45
BORCS6	BLOC-1 related complex subunit 6	0.9762	45
REC8	REC8 meiotic recombination protein	0.9762	45
B3GALT4	Beta-1,3-galactosyltransferase 4	0.9524	25
LY6G5C	Lymphocyte antigen 6 family member G5C	0.9524	45
SLC52A2	Solute carrier family 52 member 2	0.9524	45
FNTA	Farnesyltransferase, CAAX box, alpha	0.9524	25
SLC30A5	Solute carrier family 30 member 5	0.9524	25
JTB	Jumping translocation breakpoint	0.9524	45
TIMM29	Translocase of inner mitochondrial membrane 29	0.9524	45
AMDHD1	Amidohydrolase domain containing 1	0.9524	45
ID2	Inhibitor of DNA binding 2	0.9524	45
KLC1	Kinesin light chain 1	0.9286	25
CRELD1	Cysteine rich with EGF like domains 1	0.9286	25

Adipocytes	26.4 nTPM
Breast	32.1 nTPM
Adipose tissue	20.8 nTPM

Alveolar cells type 1	72.5 nTPM
Lung	72.5 nTPM

Alveolar cells type 2	85.3 nTPM
Lung	85.3 nTPM

Astrocytes	8.4 nTPM
Brain	8.4 nTPM

B-cells	36.0 nTPM
Liver	53.1 nTPM
Salivary gland	48.8 nTPM
Skin	47.4 nTPM
Lung	46.9 nTPM
Thymus	38.8 nTPM
PBMC	36.9 nTPM
Esophagus	35.4 nTPM
Spleen	31.4 nTPM
Kidney	31.2 nTPM
Stomach	27.8 nTPM
Lymph node	26.3 nTPM
Bone marrow	22.5 nTPM
Adipose tissue	21.0 nTPM

Ciliated cells	22.4 nTPM
Lung	29.3 nTPM
Fallopian tube	27.5 nTPM
Endometrium	22.8 nTPM
Bronchus	10.1 nTPM

Club cells	32.7 nTPM
Lung	54.5 nTPM
Prostate	28.3 nTPM
Bronchus	15.5 nTPM

Dendritic cells	30.8 nTPM
PBMC	32.4 nTPM
Adipose tissue	29.2 nTPM

Endothelial cells	34.7 nTPM
Fallopian tube	71.9 nTPM
Lung	57.3 nTPM
Liver	51.6 nTPM
Skin	49.4 nTPM
Thymus	42.6 nTPM
Tongue	41.7 nTPM
Placenta	38.0 nTPM
Pancreas	36.2 nTPM
Skeletal muscle	36.1 nTPM
Endometrium	32.4 nTPM
Ovary	29.0 nTPM
Testis	28.7 nTPM
Breast	24.6 nTPM
Vascular	23.3 nTPM
Prostate	21.0 nTPM
Salivary gland	19.8 nTPM
Esophagus	19.0 nTPM
Heart muscle	1.6 nTPM

Enteroendocrine cells	64.6 nTPM
Colon	125.7 nTPM
Small intestine	41.2 nTPM
Rectum	26.8 nTPM

Fibroblasts	37.3 nTPM
Pancreas	112.3 nTPM
Lung	98.7 nTPM
Fallopian tube	48.6 nTPM
Placenta	48.1 nTPM
Thymus	45.9 nTPM
Skin	32.9 nTPM
Skeletal muscle	32.4 nTPM
Adipose tissue	28.2 nTPM
Salivary gland	26.6 nTPM
Breast	26.2 nTPM
Vascular	24.8 nTPM
Stomach	23.1 nTPM
Prostate	16.5 nTPM
Esophagus	15.3 nTPM
Liver	11.9 nTPM
Heart muscle	6.2 nTPM

Granulocytes	22.3 nTPM
Lung	36.3 nTPM
Fallopian tube	25.6 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	46.1 nTPM
Colon	83.9 nTPM
Rectum	36.0 nTPM
Small intestine	18.2 nTPM

Lymphatic endothelial cells	33.1 nTPM
Fallopian tube	39.1 nTPM
Ovary	27.3 nTPM

Macrophages	41.4 nTPM
Lung	133.5 nTPM
Pancreas	106.9 nTPM
Prostate	54.2 nTPM
Kidney	45.1 nTPM
Skin	40.1 nTPM
Thymus	40.0 nTPM
Testis	38.4 nTPM
Tongue	38.4 nTPM
Breast	36.8 nTPM
Endometrium	34.4 nTPM
Fallopian tube	29.8 nTPM
Salivary gland	29.2 nTPM
Skeletal muscle	28.6 nTPM
Vascular	27.6 nTPM
Adipose tissue	27.5 nTPM
Esophagus	23.1 nTPM
Stomach	23.1 nTPM
Bone marrow	21.3 nTPM
Spleen	8.0 nTPM

Basal keratinocytes	91.1 nTPM
Skin	91.5 nTPM
Tongue	90.8 nTPM

Basal prostatic cells	30.2 nTPM
Prostate	30.2 nTPM

Basal respiratory cells	16.0 nTPM
Bronchus	16.0 nTPM

Basal squamous epithelial cells	44.3 nTPM
Esophagus	44.3 nTPM

Paneth cells	50.6 nTPM
Colon	79.6 nTPM
Rectum	48.1 nTPM
Small intestine	24.2 nTPM

Plasma cells	62.0 nTPM
Thymus	111.6 nTPM
Liver	101.6 nTPM
Spleen	93.1 nTPM
Bone marrow	60.4 nTPM
Salivary gland	42.5 nTPM
Esophagus	31.2 nTPM
Stomach	28.9 nTPM
Fallopian tube	27.0 nTPM

Schwann cells	28.4 nTPM
Adipose tissue	47.6 nTPM
Vascular	25.6 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	43.4 nTPM
Tongue	66.3 nTPM
Salivary gland	20.6 nTPM

Smooth muscle cells	35.7 nTPM
Lung	83.5 nTPM
Thymus	48.1 nTPM
Placenta	45.9 nTPM
Skeletal muscle	42.2 nTPM
Fallopian tube	42.0 nTPM
Skin	39.1 nTPM
Endometrium	36.8 nTPM
Ovary	36.5 nTPM
Breast	29.8 nTPM
Adipose tissue	29.4 nTPM
Tongue	29.3 nTPM
Salivary gland	28.4 nTPM
Vascular	24.2 nTPM
Esophagus	22.8 nTPM
Liver	17.0 nTPM
Prostate	15.8 nTPM

Suprabasal keratinocytes	86.0 nTPM
Skin	92.0 nTPM
Tongue	80.0 nTPM

T-cells	30.1 nTPM
Thymus	42.9 nTPM
Lung	41.7 nTPM
Salivary gland	39.1 nTPM
Colon	36.1 nTPM
PBMC	35.6 nTPM
Kidney	34.6 nTPM
Liver	32.3 nTPM
Tongue	32.1 nTPM
Endometrium	29.4 nTPM
Vascular	29.3 nTPM
Breast	29.0 nTPM
Lymph node	27.9 nTPM
Stomach	27.0 nTPM
Prostate	27.0 nTPM
Skin	26.6 nTPM
Fallopian tube	26.5 nTPM
Bone marrow	25.0 nTPM
Skeletal muscle	24.2 nTPM
Spleen	23.4 nTPM
Adipose tissue	22.0 nTPM
Esophagus	19.5 nTPM

Undifferentiated cells	132.1 nTPM
Colon	209.1 nTPM
Small intestine	99.0 nTPM
Rectum	88.4 nTPM

Amygdala excitatory	13.0 nTPM
Basal ganglia	15.4 nTPM
Hippocampus	13.7 nTPM
Thalamus	13.2 nTPM
Cerebral cortex	12.6 nTPM
Amygdala	12.4 nTPM
Hypothalamus	10.8 nTPM

Astrocyte	13.2 nTPM
Thalamus	16.0 nTPM
Cerebellum	15.6 nTPM
Midbrain	15.0 nTPM
Pons	14.5 nTPM
Cerebral cortex	14.3 nTPM
Medulla oblongata	13.4 nTPM
Hippocampus	13.3 nTPM
Spinal cord	12.4 nTPM
Basal ganglia	10.6 nTPM
Amygdala	10.1 nTPM
Hypothalamus	10.0 nTPM

Bergmann glia	10.3 nTPM
Cerebellum	12.2 nTPM
Pons	10.1 nTPM
Medulla oblongata	8.5 nTPM

Central nervous system macrophage	12.0 nTPM
Spinal cord	15.0 nTPM
Cerebral cortex	14.2 nTPM
Hippocampus	13.2 nTPM
Cerebellum	13.1 nTPM
Thalamus	12.6 nTPM
Midbrain	11.5 nTPM
Hypothalamus	11.2 nTPM
Pons	10.9 nTPM
Medulla oblongata	10.5 nTPM
Amygdala	10.0 nTPM
Basal ganglia	9.6 nTPM

Cerebellar inhibitory	30.1 nTPM
Midbrain	33.6 nTPM
Pons	31.4 nTPM
Spinal cord	30.2 nTPM
Cerebellum	29.6 nTPM
Medulla oblongata	25.6 nTPM

Cge interneuron	24.2 nTPM
Thalamus	29.4 nTPM
Cerebral cortex	27.2 nTPM
Basal ganglia	24.7 nTPM
Hippocampus	24.7 nTPM
Midbrain	23.6 nTPM
Amygdala	20.8 nTPM
Hypothalamus	19.0 nTPM

Choroid plexus epithelial cell	11.5 nTPM
Thalamus	13.7 nTPM
Basal ganglia	11.1 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	10.2 nTPM

Committed oligodendrocyte precursor	17.5 nTPM
Cerebral cortex	22.8 nTPM
Thalamus	22.5 nTPM
Spinal cord	22.1 nTPM
Medulla oblongata	20.7 nTPM
Cerebellum	20.6 nTPM
Hippocampus	17.1 nTPM
Basal ganglia	16.4 nTPM
Midbrain	16.0 nTPM
Pons	14.2 nTPM
Hypothalamus	11.6 nTPM
Amygdala	9.0 nTPM

Deep-layer corticothalamic and 6b	16.1 nTPM
Midbrain	20.0 nTPM
Cerebral cortex	17.0 nTPM
Hippocampus	16.5 nTPM
Basal ganglia	15.8 nTPM
Amygdala	14.4 nTPM
Hypothalamus	12.8 nTPM

Deep-layer intratelencephalic	13.9 nTPM
Cerebral cortex	17.3 nTPM
Basal ganglia	14.7 nTPM
Hippocampus	13.4 nTPM
Hypothalamus	12.4 nTPM
Amygdala	11.7 nTPM

Deep-layer near-projecting	22.0 nTPM
Basal ganglia	25.5 nTPM
Cerebral cortex	25.0 nTPM
Hippocampus	22.8 nTPM
Amygdala	18.7 nTPM
Hypothalamus	18.0 nTPM

Eccentric medium spiny neuron	14.9 nTPM
Hypothalamus	16.1 nTPM
Basal ganglia	15.5 nTPM
Cerebral cortex	15.5 nTPM
Thalamus	15.4 nTPM
Hippocampus	13.7 nTPM
Amygdala	13.1 nTPM