Single cell type - TOM1L1 - The Human Protein Atlas

TOM1L1

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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.	TOM1L1
Gene descriptionⁱ Full gene name according to HGNC.	Target of myb1 like 1 membrane trafficking protein
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.	14

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 (Late spermatids)
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.	0.52
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.	Not detected in immune cells
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 (Late spermatids)

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: Not detected in immune cells
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

TOM1L1 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.
PIP4K2C	Phosphatidylinositol-5-phosphate 4-kinase type 2 gamma	0.5117	45
IGSF22	Immunoglobulin superfamily member 22	0.4509	39
MAPK13	Mitogen-activated protein kinase 13	0.4440	17
WFDC10B	WAP four-disulfide core domain 10B	0.4288	36
NAPG	NSF attachment protein gamma	0.4149	45
CFAP221	Cilia and flagella associated protein 221	0.4104	42
NEURL1	Neuralized E3 ubiquitin protein ligase 1	0.4051	36
GALNT3	Polypeptide N-acetylgalactosaminyltransferase 3	0.4044	45
ACSM1	Acyl-CoA synthetase medium chain family member 1	0.4043	6
ZNG1F	Zn regulated GTPase metalloprotein activator 1F	0.3916	69
FSHR	Follicle stimulating hormone receptor	0.3895	34
POC1B	POC1 centriolar protein B	0.3860	37
RAB3IP	RAB3A interacting protein	0.3823	36
C6orf132	Chromosome 6 open reading frame 132	0.3815	45
MMP24OS	MMP24 opposite strand	0.3808	45

Adipocytes	1.4 nTPM
Breast	1.8 nTPM
Adipose tissue	1.0 nTPM

Alveolar cells type 1	27.0 nTPM
Lung	27.0 nTPM

Alveolar cells type 2	30.3 nTPM
Lung	30.3 nTPM

Astrocytes	14.6 nTPM
Brain	14.6 nTPM

B-cells	0.3 nTPM
Salivary gland	1.8 nTPM
Lung	1.3 nTPM
Thymus	0.5 nTPM
Adipose tissue	0.4 nTPM
Stomach	0.4 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Ciliated cells	22.1 nTPM
Endometrium	28.4 nTPM
Fallopian tube	25.2 nTPM
Lung	22.7 nTPM
Bronchus	12.1 nTPM

Club cells	22.5 nTPM
Lung	25.9 nTPM
Bronchus	22.2 nTPM
Prostate	19.3 nTPM

Endothelial cells	2.2 nTPM
Liver	8.8 nTPM
Prostate	5.5 nTPM
Tongue	5.1 nTPM
Pancreas	2.6 nTPM
Endometrium	2.4 nTPM
Salivary gland	2.2 nTPM
Thymus	2.1 nTPM
Lung	2.0 nTPM
Fallopian tube	1.7 nTPM
Heart muscle	1.5 nTPM
Ovary	1.4 nTPM
Skeletal muscle	1.1 nTPM
Vascular	1.1 nTPM
Testis	0.9 nTPM
Breast	0.9 nTPM
Esophagus	0.5 nTPM
Skin	0.4 nTPM
Placenta	0.0 nTPM

Enteroendocrine cells	24.6 nTPM
Colon	33.2 nTPM
Rectum	26.8 nTPM
Small intestine	13.7 nTPM

Fibroblasts	3.7 nTPM
Placenta	15.9 nTPM
Pancreas	7.0 nTPM
Prostate	6.6 nTPM
Lung	5.5 nTPM
Salivary gland	4.5 nTPM
Vascular	4.2 nTPM
Esophagus	3.1 nTPM
Stomach	2.9 nTPM
Thymus	2.4 nTPM
Skin	1.5 nTPM
Skeletal muscle	1.5 nTPM
Breast	1.4 nTPM
Heart muscle	1.0 nTPM
Fallopian tube	1.0 nTPM
Adipose tissue	0.4 nTPM
Liver	0.0 nTPM

Granulocytes	0.9 nTPM
Fallopian tube	2.3 nTPM
Lung	0.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	62.1 nTPM
Small intestine	76.2 nTPM
Rectum	57.1 nTPM
Colon	52.9 nTPM

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.3 nTPM
Ovary	0.0 nTPM

Macrophages	1.9 nTPM
Kidney	5.3 nTPM
Vascular	5.0 nTPM
Prostate	4.3 nTPM
Pancreas	4.1 nTPM
Tongue	4.0 nTPM
Endometrium	3.1 nTPM
Salivary gland	2.8 nTPM
Lung	2.6 nTPM
Breast	1.3 nTPM
Skin	1.1 nTPM
Thymus	0.8 nTPM
Fallopian tube	0.8 nTPM
Testis	0.6 nTPM
Adipose tissue	0.5 nTPM
Skeletal muscle	0.2 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	31.6 nTPM
Small intestine	41.4 nTPM
Rectum	38.9 nTPM
Colon	14.5 nTPM

Basal keratinocytes	18.3 nTPM
Tongue	21.3 nTPM
Skin	15.3 nTPM

Basal prostatic cells	23.8 nTPM
Prostate	23.8 nTPM

Basal respiratory cells	20.1 nTPM
Bronchus	20.1 nTPM

Basal squamous epithelial cells	24.8 nTPM
Esophagus	24.8 nTPM

Plasma cells	0.8 nTPM
Salivary gland	3.6 nTPM
Liver	1.5 nTPM
Stomach	0.4 nTPM
Thymus	0.3 nTPM
Fallopian tube	0.3 nTPM
Spleen	0.2 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	2.2 nTPM
Vascular	5.7 nTPM
Adipose tissue	0.8 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	9.8 nTPM
Salivary gland	19.6 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	6.8 nTPM
Prostate	14.6 nTPM
Lung	10.6 nTPM
Vascular	10.6 nTPM
Tongue	8.7 nTPM
Breast	8.1 nTPM
Fallopian tube	7.1 nTPM
Skin	6.8 nTPM
Placenta	6.3 nTPM
Thymus	6.2 nTPM
Ovary	6.2 nTPM
Esophagus	6.0 nTPM
Salivary gland	5.7 nTPM
Endometrium	4.5 nTPM
Adipose tissue	4.0 nTPM
Skeletal muscle	2.3 nTPM
Liver	0.8 nTPM

Suprabasal keratinocytes	24.2 nTPM
Tongue	29.4 nTPM
Skin	19.0 nTPM

T-cells	1.5 nTPM
Endometrium	6.3 nTPM
Prostate	5.7 nTPM
Kidney	3.5 nTPM
Tongue	2.3 nTPM
Breast	2.3 nTPM
Salivary gland	1.9 nTPM
Fallopian tube	1.5 nTPM
Liver	1.4 nTPM
Skeletal muscle	1.1 nTPM
Colon	1.0 nTPM
Vascular	0.8 nTPM
Skin	0.7 nTPM
Thymus	0.5 nTPM
Stomach	0.4 nTPM
PBMC	0.3 nTPM
Lymph node	0.3 nTPM
Lung	0.3 nTPM
Adipose tissue	0.2 nTPM
Spleen	0.2 nTPM
Bone marrow	0.1 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	45.5 nTPM
Small intestine	57.0 nTPM
Rectum	44.1 nTPM
Colon	35.3 nTPM

Amygdala excitatory	84.8 nTPM
Cerebral cortex	102.6 nTPM
Thalamus	96.6 nTPM
Amygdala	92.5 nTPM
Basal ganglia	89.3 nTPM
Hippocampus	88.5 nTPM
Hypothalamus	39.5 nTPM

Astrocyte	76.7 nTPM
Medulla oblongata	123.9 nTPM
Spinal cord	95.6 nTPM
Pons	95.4 nTPM
Hypothalamus	83.5 nTPM
Basal ganglia	82.9 nTPM
Midbrain	82.9 nTPM
Thalamus	82.2 nTPM
Cerebral cortex	56.5 nTPM
Hippocampus	48.4 nTPM
Cerebellum	47.3 nTPM
Amygdala	44.9 nTPM

Bergmann glia	97.4 nTPM
Medulla oblongata	110.8 nTPM
Pons	94.9 nTPM
Cerebellum	86.5 nTPM

Central nervous system macrophage	30.0 nTPM
Basal ganglia	47.6 nTPM
Medulla oblongata	38.7 nTPM
Pons	33.6 nTPM
Spinal cord	32.4 nTPM
Hypothalamus	30.7 nTPM
Thalamus	29.9 nTPM
Cerebral cortex	26.7 nTPM
Midbrain	26.1 nTPM
Cerebellum	25.0 nTPM
Hippocampus	21.2 nTPM
Amygdala	17.6 nTPM

Cerebellar inhibitory	98.6 nTPM
Spinal cord	121.0 nTPM
Medulla oblongata	119.3 nTPM
Cerebellum	97.8 nTPM
Midbrain	81.8 nTPM
Pons	73.3 nTPM

Cge interneuron	50.8 nTPM
Midbrain	65.3 nTPM
Hippocampus	61.1 nTPM
Cerebral cortex	57.4 nTPM
Basal ganglia	54.2 nTPM
Amygdala	51.4 nTPM
Thalamus	48.4 nTPM
Hypothalamus	18.1 nTPM

Choroid plexus epithelial cell	131.1 nTPM
Basal ganglia	148.9 nTPM
Hippocampus	144.2 nTPM
Medulla oblongata	138.1 nTPM
Thalamus	93.2 nTPM

Committed oligodendrocyte precursor	53.5 nTPM
Midbrain	77.3 nTPM
Medulla oblongata	74.9 nTPM
Cerebral cortex	64.0 nTPM
Pons	57.5 nTPM
Basal ganglia	55.8 nTPM
Cerebellum	55.5 nTPM
Hippocampus	53.8 nTPM
Spinal cord	47.8 nTPM
Amygdala	41.7 nTPM
Thalamus	34.4 nTPM
Hypothalamus	25.3 nTPM

Deep-layer corticothalamic and 6b	78.9 nTPM
Hippocampus	94.7 nTPM
Midbrain	94.3 nTPM
Basal ganglia	88.3 nTPM
Cerebral cortex	85.8 nTPM
Amygdala	64.3 nTPM
Hypothalamus	45.9 nTPM

Deep-layer intratelencephalic	89.3 nTPM
Basal ganglia	110.8 nTPM
Amygdala	95.7 nTPM
Cerebral cortex	89.8 nTPM
Hippocampus	88.4 nTPM
Hypothalamus	62.0 nTPM

Deep-layer near-projecting	122.1 nTPM
Hippocampus	167.8 nTPM
Basal ganglia	127.5 nTPM
Amygdala	125.4 nTPM
Cerebral cortex	114.6 nTPM
Hypothalamus	75.3 nTPM

Eccentric medium spiny neuron	75.3 nTPM
Cerebral cortex	88.1 nTPM
Basal ganglia	83.4 nTPM
Amygdala	80.5 nTPM
Thalamus	68.6 nTPM
Hippocampus	67.2 nTPM
Hypothalamus	64.1 nTPM

Endothelial cell	22.3 nTPM
Pons	34.3 nTPM
Hippocampus	28.9 nTPM
Medulla oblongata	25.6 nTPM
Midbrain	25.5 nTPM
Hypothalamus	22.3 nTPM
Thalamus	22.0 nTPM
Basal ganglia	21.4 nTPM
Cerebral cortex	20.5 nTPM
Cerebellum	20.1 nTPM
Spinal cord	17.3 nTPM
Amygdala	7.8 nTPM