Single cell type - CLTCL1 - The Human Protein Atlas

CLTCL1

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Pathway

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.	CLTCL1
Gene descriptionⁱ Full gene name according to HGNC.	Clathrin heavy chain like 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Plasma proteins 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.	5

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.	Neurons - Neuronal signaling (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, Skeletal myocytes, Early spermatids, Spermatocytes, Oligodendrocyte precursor cells, Oligodendrocytes)
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.	0.72
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.	Group enriched (neutrophil, classical monocyte)
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, Skeletal myocytes, Early spermatids, Spermatocytes, Oligodendrocyte precursor cells, Oligodendrocytes)

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: Group enriched (neutrophil, classical monocyte)
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

CLTCL1 is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
NPY5R	Neuropeptide Y receptor Y5	0.5906	69
SOBP	Sine oculis binding protein homolog	0.5542	69
PDE3A	Phosphodiesterase 3A	0.5170	69
CNR1	Cannabinoid receptor 1	0.4947	69
APOL5	Apolipoprotein L5	0.4935	69
ADRA1A	Adrenoceptor alpha 1A	0.4772	69
NMBR	Neuromedin B receptor	0.4714	69
INTS7	Integrator complex subunit 7	0.4669	70
CHRFAM7A	CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion	0.4651	69
L3MBTL4	L3MBTL histone methyl-lysine binding protein 4	0.4627	69
LRRC4B	Leucine rich repeat containing 4B	0.4450	71
FIGN	Fidgetin, microtubule severing factor	0.4448	69
FAM133A	Family with sequence similarity 133 member A	0.4430	69
SLC24A3	Solute carrier family 24 member 3	0.4401	69
INPP4B	Inositol polyphosphate-4-phosphatase type II B	0.4329	69

IMMUNE CELLS

CLTCL1 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.52
501 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.
CYP27A1	Cytochrome P450 family 27 subfamily A member 1	1.0000	38
S100A9	S100 calcium binding protein A9	1.0000	38
NOL3	Nucleolar protein 3	1.0000	38
GPR84	G protein-coupled receptor 84	1.0000	38
DNAJB5	DnaJ heat shock protein family (Hsp40) member B5	1.0000	38
SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	1.0000	38
FSCN1	Fascin actin-bundling protein 1	1.0000	38
PBLD	Phenazine biosynthesis like protein domain containing	0.9762	38
LRAT	Lecithin retinol acyltransferase	0.9762	38
F13A1	Coagulation factor XIII A chain	0.9762	38
RXFP2	Relaxin family peptide receptor 2	0.9762	38
VCAN	Versican	0.9762	38
ABCC6	ATP binding cassette subfamily C member 6	0.9762	38
FXYD6	FXYD domain containing ion transport regulator 6	0.9762	38
CYP1B1	Cytochrome P450 family 1 subfamily B member 1	0.9762	38

Adipocytes	1.5 nTPM
Adipose tissue	1.8 nTPM
Breast	1.2 nTPM

Alveolar cells type 1	1.1 nTPM
Lung	1.1 nTPM

Alveolar cells type 2	0.4 nTPM
Lung	0.4 nTPM

Astrocytes	9.0 nTPM
Brain	9.0 nTPM

B-cells	0.2 nTPM
Skin	1.7 nTPM
Bone marrow	0.7 nTPM
Lymph node	0.4 nTPM
Salivary gland	0.3 nTPM
Thymus	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	1.6 nTPM
Bronchus	2.7 nTPM
Lung	2.0 nTPM
Endometrium	1.4 nTPM
Fallopian tube	0.5 nTPM

Club cells	1.0 nTPM
Lung	1.5 nTPM
Bronchus	1.0 nTPM
Prostate	0.4 nTPM

Endothelial cells	1.0 nTPM
Vascular	2.3 nTPM
Thymus	2.2 nTPM
Prostate	1.9 nTPM
Salivary gland	1.8 nTPM
Liver	1.3 nTPM
Esophagus	1.3 nTPM
Skeletal muscle	1.2 nTPM
Tongue	1.2 nTPM
Ovary	1.2 nTPM
Heart muscle	0.9 nTPM
Fallopian tube	0.8 nTPM
Endometrium	0.7 nTPM
Lung	0.7 nTPM
Skin	0.1 nTPM
Testis	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.2 nTPM
Colon	0.7 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	1.5 nTPM
Heart muscle	3.2 nTPM
Thymus	3.2 nTPM
Esophagus	2.1 nTPM
Pancreas	2.0 nTPM
Vascular	1.7 nTPM
Salivary gland	1.6 nTPM
Stomach	1.4 nTPM
Liver	1.2 nTPM
Adipose tissue	1.2 nTPM
Lung	1.2 nTPM
Breast	1.2 nTPM
Placenta	1.1 nTPM
Fallopian tube	0.9 nTPM
Skeletal muscle	0.8 nTPM
Skin	0.7 nTPM
Prostate	0.0 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.2 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.6 nTPM
Rectum	1.5 nTPM
Colon	0.2 nTPM
Small intestine	0.1 nTPM

Lymphatic endothelial cells	0.5 nTPM
Fallopian tube	1.0 nTPM
Ovary	0.0 nTPM

Macrophages	0.7 nTPM
Tongue	1.6 nTPM
Esophagus	1.3 nTPM
Endometrium	1.2 nTPM
Fallopian tube	1.1 nTPM
Skeletal muscle	1.0 nTPM
Bone marrow	1.0 nTPM
Spleen	1.0 nTPM
Prostate	1.0 nTPM
Testis	0.6 nTPM
Salivary gland	0.6 nTPM
Thymus	0.6 nTPM
Vascular	0.6 nTPM
Lung	0.4 nTPM
Adipose tissue	0.3 nTPM
Breast	0.1 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.9 nTPM
Rectum	2.7 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Cone photoreceptor cells	3.4 nTPM
Eye	3.4 nTPM

Plasma cells	0.2 nTPM
Fallopian tube	0.6 nTPM
Spleen	0.5 nTPM
Thymus	0.4 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM

Schwann cells	0.5 nTPM
Vascular	1.6 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.3 nTPM
Salivary gland	0.6 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	5.5 nTPM
Thymus	14.6 nTPM
Adipose tissue	9.1 nTPM
Prostate	8.5 nTPM
Esophagus	8.4 nTPM
Vascular	7.6 nTPM
Skeletal muscle	7.1 nTPM
Salivary gland	5.1 nTPM
Endometrium	5.0 nTPM
Breast	4.9 nTPM
Ovary	4.2 nTPM
Lung	3.5 nTPM
Tongue	3.3 nTPM
Skin	2.7 nTPM
Placenta	1.8 nTPM
Fallopian tube	1.8 nTPM
Liver	0.8 nTPM

T-cells	0.2 nTPM
Vascular	1.2 nTPM
Endometrium	0.6 nTPM
Skin	0.4 nTPM
Prostate	0.4 nTPM
Tongue	0.4 nTPM
Stomach	0.3 nTPM
Breast	0.3 nTPM
Spleen	0.2 nTPM
Thymus	0.2 nTPM
Fallopian tube	0.2 nTPM
PBMC	0.1 nTPM
Adipose tissue	0.1 nTPM
Bone marrow	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM

Undifferentiated cells	0.9 nTPM
Rectum	2.0 nTPM
Colon	0.4 nTPM
Small intestine	0.3 nTPM

Amygdala excitatory	19.8 nTPM
Thalamus	39.0 nTPM
Hypothalamus	29.4 nTPM
Basal ganglia	17.1 nTPM
Hippocampus	11.9 nTPM
Cerebral cortex	11.8 nTPM
Amygdala	9.5 nTPM

Astrocyte	52.1 nTPM
Cerebellum	71.7 nTPM
Midbrain	69.0 nTPM
Pons	67.1 nTPM
Medulla oblongata	60.9 nTPM
Spinal cord	59.6 nTPM
Hypothalamus	57.3 nTPM
Thalamus	48.2 nTPM
Basal ganglia	37.6 nTPM
Amygdala	37.5 nTPM
Hippocampus	36.2 nTPM
Cerebral cortex	28.0 nTPM

Bergmann glia	15.5 nTPM
Cerebellum	21.5 nTPM
Pons	14.4 nTPM
Medulla oblongata	10.7 nTPM

Central nervous system macrophage	6.5 nTPM
Thalamus	9.6 nTPM
Hypothalamus	7.5 nTPM
Amygdala	7.0 nTPM
Hippocampus	6.9 nTPM
Midbrain	6.7 nTPM
Basal ganglia	6.5 nTPM
Cerebellum	6.1 nTPM
Medulla oblongata	6.1 nTPM
Cerebral cortex	5.5 nTPM
Pons	5.3 nTPM
Spinal cord	4.7 nTPM

Cerebellar inhibitory	37.7 nTPM
Midbrain	45.7 nTPM
Medulla oblongata	42.4 nTPM
Pons	33.9 nTPM
Cerebellum	33.3 nTPM
Spinal cord	33.0 nTPM

Cge interneuron	36.3 nTPM
Hypothalamus	60.3 nTPM
Amygdala	41.9 nTPM
Basal ganglia	37.9 nTPM
Cerebral cortex	34.2 nTPM
Hippocampus	32.2 nTPM
Midbrain	27.7 nTPM
Thalamus	20.2 nTPM

Choroid plexus epithelial cell	28.9 nTPM
Basal ganglia	49.5 nTPM
Medulla oblongata	24.8 nTPM
Thalamus	21.9 nTPM
Hippocampus	19.4 nTPM

Committed oligodendrocyte precursor	28.7 nTPM
Thalamus	49.5 nTPM
Spinal cord	44.1 nTPM
Cerebellum	34.9 nTPM
Amygdala	29.9 nTPM
Cerebral cortex	29.8 nTPM
Hypothalamus	28.7 nTPM
Medulla oblongata	20.7 nTPM
Midbrain	20.2 nTPM
Hippocampus	19.9 nTPM
Pons	19.5 nTPM
Basal ganglia	18.6 nTPM

Deep-layer corticothalamic and 6b	39.7 nTPM
Hypothalamus	46.1 nTPM
Amygdala	44.6 nTPM
Hippocampus	38.6 nTPM
Basal ganglia	37.9 nTPM
Midbrain	36.6 nTPM
Cerebral cortex	34.2 nTPM

Deep-layer intratelencephalic	22.3 nTPM
Hypothalamus	30.1 nTPM
Amygdala	28.0 nTPM
Basal ganglia	20.9 nTPM
Cerebral cortex	17.3 nTPM
Hippocampus	15.2 nTPM

Deep-layer near-projecting	16.3 nTPM
Hypothalamus	24.2 nTPM
Basal ganglia	20.0 nTPM
Amygdala	18.7 nTPM
Cerebral cortex	10.2 nTPM
Hippocampus	8.5 nTPM

Eccentric medium spiny neuron	11.0 nTPM
Hippocampus	13.3 nTPM
Hypothalamus	12.5 nTPM
Basal ganglia	12.0 nTPM
Thalamus	11.0 nTPM
Cerebral cortex	9.2 nTPM
Amygdala	8.1 nTPM

Endothelial cell	18.2 nTPM
Amygdala	31.3 nTPM
Basal ganglia	25.2 nTPM
Thalamus	22.0 nTPM
Midbrain	18.9 nTPM
Cerebellum	18.6 nTPM
Pons	18.1 nTPM
Hippocampus	16.7 nTPM
Cerebral cortex	14.1 nTPM
Medulla oblongata	13.3 nTPM
Hypothalamus	11.2 nTPM
Spinal cord	10.4 nTPM

Ependymal cell	43.0 nTPM
Basal ganglia	52.9 nTPM
Amygdala	51.2 nTPM
Hippocampus	50.3 nTPM
Thalamus	44.5 nTPM
Pons	43.2 nTPM
Hypothalamus	41.0 nTPM
Medulla oblongata	38.6 nTPM
Midbrain	36.8 nTPM
Spinal cord	28.7 nTPM