Single cell type - CHMP1B - The Human Protein Atlas

CHMP1B

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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.	CHMP1B
Gene descriptionⁱ Full gene name according to HGNC.	Charged multivesicular body protein 1B
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.	1

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.	Monocytes - Innate immune response (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, Langerhans cells)
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.	0.40
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.	Not detected
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, Langerhans cells)

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: Not detected

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

CHMP1B is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.95
447 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.
SERPINB9	Serpin family B member 9	0.7616	28
IRAK2	Interleukin 1 receptor associated kinase 2	0.7396	29
OR2B11	Olfactory receptor family 2 subfamily B member 11	0.7386	29
RILPL2	Rab interacting lysosomal protein like 2	0.7355	29
NLRP3	NLR family pyrin domain containing 3	0.7290	29
REL	REL proto-oncogene, NF-kB subunit	0.7175	29
CYSLTR2	Cysteinyl leukotriene receptor 2	0.7150	29
STX11	Syntaxin 11	0.7069	29
MAP3K8	Mitogen-activated protein kinase kinase kinase 8	0.7014	29
GNA13	G protein subunit alpha 13	0.7014	28
GPR132	G protein-coupled receptor 132	0.7002	29
RASGEF1B	RasGEF domain family member 1B	0.7001	29
NFKB1	Nuclear factor kappa B subunit 1	0.6930	29
ETV3	ETS variant transcription factor 3	0.6859	28
IL20	Interleukin 20	0.6837	12

IMMUNE CELLS

CHMP1B is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 1
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.
NFAM1	NFAT activating protein with ITAM motif 1	1.0000	38
VAMP3	Vesicle associated membrane protein 3	1.0000	38
NPEPL1	Aminopeptidase like 1	1.0000	38
TNFAIP2	TNF alpha induced protein 2	1.0000	38
P2RY13	Purinergic receptor P2Y13	1.0000	38
CLEC7A	C-type lectin domain containing 7A	1.0000	38
PLB1	Phospholipase B1	1.0000	38
MVP	Major vault protein	1.0000	38
SIGLEC9	Sialic acid binding Ig like lectin 9	0.9762	38
SQOR	Sulfide quinone oxidoreductase	0.9762	38
TLR2	Toll like receptor 2	0.9762	38
LCP1	Lymphocyte cytosolic protein 1	0.9762	38
TM9SF2	Transmembrane 9 superfamily member 2	0.9762	38
TMEM30A	Transmembrane protein 30A	0.9762	37
CPPED1	Calcineurin like phosphoesterase domain containing 1	0.9762	37

Adipocytes	69.3 nTPM
Adipose tissue	71.4 nTPM
Breast	67.2 nTPM

Alveolar cells type 1	39.1 nTPM
Lung	39.1 nTPM

Alveolar cells type 2	34.9 nTPM
Lung	34.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	114.7 nTPM
Adipose tissue	257.6 nTPM
Skin	257.5 nTPM
Stomach	159.0 nTPM
Lymph node	143.7 nTPM
Spleen	138.1 nTPM
Esophagus	88.5 nTPM
PBMC	83.1 nTPM
Liver	82.1 nTPM
Kidney	78.0 nTPM
Thymus	66.1 nTPM
Salivary gland	65.8 nTPM
Lung	61.7 nTPM
Bone marrow	10.2 nTPM

Basal squamous epithelial cells	234.0 nTPM
Esophagus	234.0 nTPM

Ciliated cells	86.6 nTPM
Endometrium	146.0 nTPM
Bronchus	122.5 nTPM
Fallopian tube	40.8 nTPM
Lung	37.2 nTPM

Club cells	128.7 nTPM
Bronchus	238.2 nTPM
Lung	90.4 nTPM
Prostate	57.4 nTPM

Dendritic cells	171.1 nTPM
Adipose tissue	302.6 nTPM
PBMC	39.6 nTPM

Endothelial cells	59.3 nTPM
Endometrium	169.8 nTPM
Pancreas	118.9 nTPM
Breast	85.2 nTPM
Prostate	83.2 nTPM
Placenta	81.2 nTPM
Skin	75.5 nTPM
Tongue	53.4 nTPM
Skeletal muscle	51.0 nTPM
Testis	48.5 nTPM
Ovary	46.1 nTPM
Salivary gland	43.2 nTPM
Esophagus	41.4 nTPM
Liver	35.3 nTPM
Lung	32.9 nTPM
Fallopian tube	29.7 nTPM
Vascular	29.1 nTPM
Thymus	24.8 nTPM
Heart muscle	17.7 nTPM

Enteroendocrine cells	108.3 nTPM
Small intestine	123.6 nTPM
Colon	122.5 nTPM
Rectum	78.8 nTPM

Fibroblasts	69.0 nTPM
Placenta	187.8 nTPM
Fallopian tube	111.2 nTPM
Prostate	110.9 nTPM
Stomach	106.6 nTPM
Skin	72.8 nTPM
Skeletal muscle	67.9 nTPM
Pancreas	66.9 nTPM
Adipose tissue	61.4 nTPM
Thymus	55.4 nTPM
Esophagus	51.9 nTPM
Breast	43.0 nTPM
Vascular	41.9 nTPM
Liver	41.5 nTPM
Salivary gland	40.6 nTPM
Heart muscle	25.3 nTPM
Lung	19.3 nTPM

Granulocytes	101.0 nTPM
Tongue	135.8 nTPM
Fallopian tube	94.0 nTPM
Lung	73.1 nTPM

Intestinal goblet cells	98.3 nTPM
Small intestine	125.3 nTPM
Colon	93.3 nTPM
Rectum	76.4 nTPM

Lymphatic endothelial cells	61.1 nTPM
Fallopian tube	67.7 nTPM
Ovary	54.6 nTPM

Cholangiocytes	55.3 nTPM
Liver	55.3 nTPM

Collecting duct cells	126.4 nTPM
Kidney	126.4 nTPM

Cone photoreceptor cells	25.5 nTPM
Eye	25.5 nTPM

Cytotrophoblasts	132.9 nTPM
Placenta	132.9 nTPM

Macrophages	331.7 nTPM
Adipose tissue	1709.3 nTPM
Skin	556.0 nTPM
Breast	551.9 nTPM
Stomach	542.7 nTPM
Fallopian tube	400.7 nTPM
Esophagus	391.7 nTPM
Endometrium	366.5 nTPM
Spleen	357.9 nTPM
Skeletal muscle	349.4 nTPM
Tongue	231.8 nTPM
Prostate	203.7 nTPM
Kidney	145.1 nTPM
Pancreas	100.7 nTPM
Testis	80.6 nTPM
Lung	80.3 nTPM
Salivary gland	76.8 nTPM
Thymus	62.6 nTPM
Vascular	55.2 nTPM
Bone marrow	38.5 nTPM

Paneth cells	192.4 nTPM
Colon	249.7 nTPM
Small intestine	214.1 nTPM
Rectum	113.4 nTPM

Plasma cells	18.0 nTPM
Salivary gland	30.4 nTPM
Fallopian tube	29.3 nTPM
Stomach	28.9 nTPM
Liver	24.5 nTPM
Thymus	13.6 nTPM
Spleen	9.1 nTPM
Esophagus	5.2 nTPM
Bone marrow	3.0 nTPM

Schwann cells	431.3 nTPM
Adipose tissue	1250.0 nTPM
Vascular	31.9 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	53.2 nTPM
Tongue	57.4 nTPM
Salivary gland	48.9 nTPM

Smooth muscle cells	70.8 nTPM
Fallopian tube	181.9 nTPM
Skin	164.8 nTPM
Prostate	138.7 nTPM
Endometrium	81.9 nTPM
Placenta	76.1 nTPM
Skeletal muscle	54.3 nTPM
Tongue	53.3 nTPM
Adipose tissue	52.6 nTPM
Ovary	47.8 nTPM
Liver	47.5 nTPM
Salivary gland	45.9 nTPM
Breast	40.7 nTPM
Esophagus	38.4 nTPM
Lung	37.6 nTPM
Thymus	35.6 nTPM
Vascular	35.6 nTPM

Suprabasal keratinocytes	298.4 nTPM
Skin	509.7 nTPM
Tongue	87.1 nTPM

T-cells	131.0 nTPM
Breast	403.5 nTPM
Colon	308.1 nTPM
Adipose tissue	251.8 nTPM
Endometrium	162.7 nTPM
Prostate	150.5 nTPM
Skin	145.4 nTPM
Spleen	145.4 nTPM
Skeletal muscle	138.4 nTPM
Lymph node	122.2 nTPM
Fallopian tube	119.2 nTPM
Thymus	109.2 nTPM
Salivary gland	89.6 nTPM
Tongue	84.0 nTPM
Liver	83.2 nTPM
Esophagus	80.3 nTPM
Kidney	76.3 nTPM
Stomach	69.1 nTPM
Lung	66.5 nTPM
PBMC	65.5 nTPM
Vascular	61.9 nTPM
Bone marrow	17.4 nTPM

Undifferentiated cells	72.9 nTPM
Small intestine	85.9 nTPM
Colon	72.5 nTPM
Rectum	60.2 nTPM

Amygdala excitatory	0.2 nTPM
Cerebral cortex	0.4 nTPM
Hippocampus	0.4 nTPM
Amygdala	0.3 nTPM
Hypothalamus	0.2 nTPM
Basal ganglia	0.1 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.2 nTPM
Cerebellum	0.4 nTPM
Basal ganglia	0.3 nTPM
Midbrain	0.3 nTPM
Cerebral cortex	0.2 nTPM
Thalamus	0.2 nTPM
Amygdala	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.1 nTPM
Medulla oblongata	0.1 nTPM
Pons	0.1 nTPM
Spinal cord	0.1 nTPM

Bergmann glia	0.6 nTPM
Pons	1.4 nTPM
Cerebellum	0.5 nTPM
Medulla oblongata	0.0 nTPM

Central nervous system macrophage	0.7 nTPM
Spinal cord	1.8 nTPM
Medulla oblongata	1.0 nTPM
Cerebellum	0.9 nTPM
Basal ganglia	0.8 nTPM
Hippocampus	0.8 nTPM
Amygdala	0.7 nTPM
Midbrain	0.7 nTPM
Cerebral cortex	0.5 nTPM
Hypothalamus	0.4 nTPM
Thalamus	0.4 nTPM
Pons	0.3 nTPM

Cerebellar inhibitory	0.1 nTPM
Cerebellum	0.3 nTPM
Midbrain	0.3 nTPM
Pons	0.1 nTPM
Medulla oblongata	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.2 nTPM
Hypothalamus	0.3 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Midbrain	0.2 nTPM
Thalamus	0.1 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Medulla oblongata	0.4 nTPM
Basal ganglia	0.1 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Hypothalamus	1.4 nTPM
Cerebral cortex	0.6 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.3 nTPM
Basal ganglia	0.5 nTPM
Cerebral cortex	0.4 nTPM
Amygdala	0.3 nTPM
Hippocampus	0.3 nTPM
Hypothalamus	0.1 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.3 nTPM
Amygdala	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.3 nTPM
Hypothalamus	0.3 nTPM
Basal ganglia	0.2 nTPM

Deep-layer near-projecting	0.3 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.4 nTPM
Hippocampus	0.3 nTPM
Cerebral cortex	0.2 nTPM
Hypothalamus	0.0 nTPM