Single cell type - VPS33B - The Human Protein Atlas

VPS33B

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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.	VPS33B
Gene descriptionⁱ Full gene name according to HGNC.	VPS33B late endosome and lysosome associated
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes
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.	2

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.	Cytotrophoblasts - Mitochondria (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.	Low cell type specificity
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.	0.45
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: Low cell type specificity

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

VPS33B is part of cluster 24 Cytotrophoblasts - Mitochondria with confidenceⁱ 1
235 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.
FADD	Fas associated via death domain	0.6508	24
VIPAS39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	0.5802	24
SLC35B4	Solute carrier family 35 member B4	0.5705	24
NME6	NME/NM23 nucleoside diphosphate kinase 6	0.5694	24
VSTM5	V-set and transmembrane domain containing 5	0.5570	24
MANSC4	MANSC domain containing 4	0.5212	24
APEX2	Apurinic/apyrimidinic endodeoxyribonuclease 2	0.5146	24
SLC29A2	Solute carrier family 29 member 2	0.5097	24
RNF26	Ring finger protein 26	0.5088	4
MUL1	Mitochondrial E3 ubiquitin protein ligase 1	0.5022	39
AMELY	Amelogenin Y-linked	0.5020	24
ZFYVE19	Zinc finger FYVE-type containing 19	0.5005	24
CPSF4	Cleavage and polyadenylation specific factor 4	0.4998	24
MDFI	MyoD family inhibitor	0.4990	24
ELAC2	ElaC ribonuclease Z 2	0.4917	24

IMMUNE CELLS

VPS33B 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.
SCO1	Synthesis of cytochrome C oxidase 1	1.0000	29
SLC38A7	Solute carrier family 38 member 7	0.9762	29
CCDC124	Coiled-coil domain containing 124	0.9762	29
JOSD2	Josephin domain containing 2	0.9524	29
PHKG2	Phosphorylase kinase catalytic subunit gamma 2	0.9524	25
ANAPC15	Anaphase promoting complex subunit 15	0.9524	29
ADPRS	ADP-ribosylserine hydrolase	0.9286	29
POLR2J3	RNA polymerase II subunit J3	0.9286	29
UBE2L3	Ubiquitin conjugating enzyme E2 L3	0.9286	29
GAK	Cyclin G associated kinase	0.9286	25
CHRFAM7A	CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion	0.9286	29
SERPINB6	Serpin family B member 6	0.9286	29
ENY2	ENY2 transcription and export complex 2 subunit	0.9286	29
NDUFB2	NADH:ubiquinone oxidoreductase subunit B2	0.9286	29
COQ9	Coenzyme Q9	0.9048	29

Adipocytes	2.1 nTPM
Breast	2.5 nTPM
Adipose tissue	1.8 nTPM

Alveolar cells type 1	3.8 nTPM
Lung	3.8 nTPM

Alveolar cells type 2	3.4 nTPM
Lung	3.4 nTPM

Astrocytes	5.3 nTPM
Brain	5.3 nTPM

B-cells	3.8 nTPM
Kidney	10.4 nTPM
Lung	8.0 nTPM
PBMC	6.2 nTPM
Salivary gland	5.4 nTPM
Adipose tissue	3.7 nTPM
Spleen	3.4 nTPM
Bone marrow	3.0 nTPM
Stomach	3.0 nTPM
Lymph node	2.0 nTPM
Thymus	2.0 nTPM
Skin	1.7 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	4.5 nTPM
Lung	5.3 nTPM
Bronchus	5.1 nTPM
Fallopian tube	4.4 nTPM
Endometrium	3.4 nTPM

Club cells	4.5 nTPM
Bronchus	5.1 nTPM
Prostate	4.3 nTPM
Lung	4.1 nTPM

Endothelial cells	3.8 nTPM
Liver	8.8 nTPM
Pancreas	7.8 nTPM
Lung	5.9 nTPM
Placenta	5.7 nTPM
Testis	4.9 nTPM
Vascular	4.2 nTPM
Prostate	3.6 nTPM
Skeletal muscle	3.5 nTPM
Skin	3.1 nTPM
Esophagus	3.0 nTPM
Salivary gland	2.8 nTPM
Fallopian tube	2.8 nTPM
Ovary	2.7 nTPM
Tongue	2.6 nTPM
Breast	2.6 nTPM
Thymus	2.2 nTPM
Endometrium	1.8 nTPM
Heart muscle	1.1 nTPM

Enteroendocrine cells	3.7 nTPM
Colon	4.3 nTPM
Small intestine	3.4 nTPM
Rectum	3.4 nTPM

Fibroblasts	3.0 nTPM
Placenta	8.8 nTPM
Pancreas	5.9 nTPM
Liver	4.7 nTPM
Vascular	3.7 nTPM
Lung	3.5 nTPM
Salivary gland	3.4 nTPM
Adipose tissue	3.2 nTPM
Skeletal muscle	3.0 nTPM
Breast	2.9 nTPM
Skin	2.3 nTPM
Prostate	2.0 nTPM
Thymus	1.6 nTPM
Fallopian tube	1.3 nTPM
Esophagus	1.1 nTPM
Heart muscle	0.3 nTPM
Stomach	0.0 nTPM

Granulocytes	3.3 nTPM
Lung	7.1 nTPM
Fallopian tube	2.9 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	5.0 nTPM
Rectum	6.8 nTPM
Colon	6.4 nTPM
Small intestine	1.7 nTPM

Lymphatic endothelial cells	1.0 nTPM
Fallopian tube	1.9 nTPM
Ovary	0.0 nTPM

Macrophages	3.9 nTPM
Lung	7.5 nTPM
Kidney	7.1 nTPM
Testis	6.8 nTPM
Skin	6.7 nTPM
Skeletal muscle	4.8 nTPM
Tongue	4.2 nTPM
Vascular	4.1 nTPM
Prostate	3.8 nTPM
Salivary gland	3.8 nTPM
Breast	3.5 nTPM
Adipose tissue	3.1 nTPM
Thymus	3.1 nTPM
Bone marrow	3.0 nTPM
Fallopian tube	2.7 nTPM
Esophagus	2.6 nTPM
Stomach	2.6 nTPM
Pancreas	2.1 nTPM
Endometrium	1.8 nTPM
Spleen	0.0 nTPM

Paneth cells	3.6 nTPM
Rectum	7.0 nTPM
Colon	3.6 nTPM
Small intestine	0.0 nTPM

Basal squamous epithelial cells	0.4 nTPM
Esophagus	0.4 nTPM

Plasma cells	2.7 nTPM
Bone marrow	6.0 nTPM
Liver	5.0 nTPM
Salivary gland	3.1 nTPM
Stomach	2.5 nTPM
Spleen	2.2 nTPM
Thymus	2.2 nTPM
Fallopian tube	0.6 nTPM
Esophagus	0.0 nTPM

Schwann cells	1.9 nTPM
Vascular	4.2 nTPM
Adipose tissue	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	1.8 nTPM
Salivary gland	3.5 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.7 nTPM
Liver	5.1 nTPM
Placenta	4.7 nTPM
Vascular	3.4 nTPM
Fallopian tube	3.4 nTPM
Adipose tissue	3.1 nTPM
Salivary gland	3.1 nTPM
Tongue	3.0 nTPM
Breast	3.0 nTPM
Ovary	2.8 nTPM
Skeletal muscle	2.4 nTPM
Thymus	2.1 nTPM
Endometrium	1.7 nTPM
Skin	1.7 nTPM
Esophagus	1.2 nTPM
Lung	1.2 nTPM
Prostate	0.6 nTPM

T-cells	4.0 nTPM
PBMC	7.6 nTPM
Liver	6.0 nTPM
Kidney	5.3 nTPM
Lung	5.0 nTPM
Colon	4.9 nTPM
Adipose tissue	4.8 nTPM
Bone marrow	4.8 nTPM
Salivary gland	4.2 nTPM
Prostate	3.9 nTPM
Spleen	3.8 nTPM
Stomach	3.8 nTPM
Vascular	3.6 nTPM
Fallopian tube	3.6 nTPM
Skin	3.5 nTPM
Tongue	3.5 nTPM
Skeletal muscle	3.4 nTPM
Endometrium	2.8 nTPM
Breast	2.8 nTPM
Esophagus	2.4 nTPM
Thymus	2.4 nTPM
Lymph node	2.2 nTPM

Undifferentiated cells	4.9 nTPM
Colon	6.0 nTPM
Small intestine	4.9 nTPM
Rectum	3.6 nTPM

Amygdala excitatory	0.5 nTPM
Thalamus	0.9 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.4 nTPM
Cerebral cortex	0.4 nTPM
Hippocampus	0.4 nTPM
Hypothalamus	0.2 nTPM

Astrocyte	0.4 nTPM
Cerebral cortex	0.6 nTPM
Cerebellum	0.5 nTPM
Pons	0.5 nTPM
Thalamus	0.5 nTPM
Basal ganglia	0.4 nTPM
Hippocampus	0.4 nTPM
Medulla oblongata	0.4 nTPM
Midbrain	0.4 nTPM
Amygdala	0.2 nTPM
Hypothalamus	0.2 nTPM
Spinal cord	0.1 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.3 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.3 nTPM
Basal ganglia	0.5 nTPM
Cerebral cortex	0.5 nTPM
Amygdala	0.4 nTPM
Medulla oblongata	0.4 nTPM
Midbrain	0.4 nTPM
Cerebellum	0.3 nTPM
Hippocampus	0.3 nTPM
Pons	0.3 nTPM
Thalamus	0.2 nTPM
Hypothalamus	0.1 nTPM
Spinal cord	0.0 nTPM

Cerebellar inhibitory	0.3 nTPM
Cerebellum	0.6 nTPM
Midbrain	0.6 nTPM
Medulla oblongata	0.2 nTPM
Pons	0.2 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.5 nTPM
Midbrain	0.7 nTPM
Basal ganglia	0.6 nTPM
Hippocampus	0.6 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Thalamus	0.5 nTPM
Hypothalamus	0.2 nTPM

Choroid plexus epithelial cell	0.2 nTPM
Medulla oblongata	0.7 nTPM
Basal ganglia	0.3 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.2 nTPM
Medulla oblongata	1.3 nTPM
Pons	0.9 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

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

Deep-layer intratelencephalic	0.4 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.4 nTPM
Cerebral cortex	0.4 nTPM
Hippocampus	0.4 nTPM
Hypothalamus	0.1 nTPM

Deep-layer near-projecting	0.6 nTPM
Hippocampus	1.3 nTPM
Amygdala	0.7 nTPM
Basal ganglia	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.3 nTPM
Cerebral cortex	0.5 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.4 nTPM
Basal ganglia	0.3 nTPM
Thalamus	0.2 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	0.1 nTPM
Cerebral cortex	1.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Ependymal cell	0.1 nTPM
Amygdala	0.6 nTPM
Hippocampus	0.4 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM