Single cell type - HPS5 - The Human Protein Atlas

HPS5

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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.	HPS5
Gene descriptionⁱ Full gene name according to HGNC.	HPS5 biogenesis of lysosomal organelles complex 2 subunit 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes Plasma proteins
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.	Dendritic cells - Antigen presentation (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 (Mucus glandular cells, Schwann 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.	0.39
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 (Mucus glandular cells, Schwann 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: 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

HPS5 is part of cluster 28 Dendritic cells - Antigen presentation with confidenceⁱ 1
245 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.
TSPAN33	Tetraspanin 33	0.6240	28
HLA-DQA1	Major histocompatibility complex, class II, DQ alpha 1	0.6139	28
CD74	CD74 molecule	0.6030	28
HLA-DRA	Major histocompatibility complex, class II, DR alpha	0.5948	28
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1	0.5928	28
HLA-DRB1	Major histocompatibility complex, class II, DR beta 1	0.5906	28
HLA-DPA1	Major histocompatibility complex, class II, DP alpha 1	0.5889	28
HLA-DMA	Major histocompatibility complex, class II, DM alpha	0.5888	28
CD83	CD83 molecule	0.5887	28
HLA-DPB1	Major histocompatibility complex, class II, DP beta 1	0.5679	28
HLA-DOA	Major histocompatibility complex, class II, DO alpha	0.5646	28
CD1C	CD1c molecule	0.5634	28
FCGR2C	Fc gamma receptor IIc (gene/pseudogene)	0.5584	58
CIITA	Class II major histocompatibility complex transactivator	0.5562	28
CLEC10A	C-type lectin domain containing 10A	0.5521	28

IMMUNE CELLS

HPS5 is part of cluster 23 B-cells - Immunoglobulins with confidenceⁱ 0.5
208 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.
GRK3	G protein-coupled receptor kinase 3	0.9762	23
BCL2L2-PABPN1	BCL2L2-PABPN1 readthrough	0.9762	23
GANC	Glucosidase alpha, neutral C	0.9762	23
CIAO2A	Cytosolic iron-sulfur assembly component 2A	0.9762	23
GSTZ1	Glutathione S-transferase zeta 1	0.9762	23
PTPRO	Protein tyrosine phosphatase receptor type O	0.9524	23
DRAM2	DNA damage regulated autophagy modulator 2	0.9524	23
UBE2E2	Ubiquitin conjugating enzyme E2 E2	0.9524	23
VAV2	Vav guanine nucleotide exchange factor 2	0.9286	23
GATD1	Glutamine amidotransferase class 1 domain containing 1	0.9286	23
C20orf96	Chromosome 20 open reading frame 96	0.9286	23
TGM2	Transglutaminase 2	0.9286	23
TTC7A	Tetratricopeptide repeat domain 7A	0.9286	23
TBC1D9	TBC1 domain family member 9	0.9048	23
ASPHD2	Aspartate beta-hydroxylase domain containing 2	0.9048	23

Adipocytes	15.9 nTPM
Breast	17.0 nTPM
Adipose tissue	14.8 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	10.7 nTPM
Lung	10.7 nTPM

Astrocytes	12.4 nTPM
Brain	12.4 nTPM

B-cells	29.0 nTPM
Spleen	44.4 nTPM
Lymph node	43.5 nTPM
Stomach	38.8 nTPM
Esophagus	35.4 nTPM
Bone marrow	32.6 nTPM
Skin	30.5 nTPM
Liver	29.0 nTPM
Adipose tissue	27.6 nTPM
Salivary gland	26.5 nTPM
Thymus	25.2 nTPM
PBMC	16.9 nTPM
Lung	16.1 nTPM
Kidney	10.4 nTPM

Ciliated cells	16.9 nTPM
Bronchus	25.8 nTPM
Endometrium	19.8 nTPM
Lung	11.2 nTPM
Fallopian tube	10.9 nTPM

Club cells	14.8 nTPM
Bronchus	19.8 nTPM
Lung	14.4 nTPM
Prostate	10.2 nTPM

Dendritic cells	18.6 nTPM
Adipose tissue	22.7 nTPM
PBMC	14.4 nTPM

Endothelial cells	11.7 nTPM
Vascular	17.0 nTPM
Heart muscle	16.1 nTPM
Esophagus	15.9 nTPM
Salivary gland	15.5 nTPM
Skeletal muscle	14.7 nTPM
Prostate	14.2 nTPM
Fallopian tube	13.6 nTPM
Lung	13.3 nTPM
Endometrium	12.7 nTPM
Thymus	12.4 nTPM
Tongue	10.5 nTPM
Pancreas	10.3 nTPM
Testis	9.2 nTPM
Ovary	9.2 nTPM
Skin	8.6 nTPM
Liver	7.6 nTPM
Breast	5.3 nTPM
Placenta	4.0 nTPM

Enteroendocrine cells	5.2 nTPM
Rectum	6.7 nTPM
Colon	5.3 nTPM
Small intestine	3.4 nTPM

Fibroblasts	12.0 nTPM
Heart muscle	28.7 nTPM
Vascular	19.8 nTPM
Esophagus	16.0 nTPM
Salivary gland	15.3 nTPM
Lung	12.6 nTPM
Thymus	11.5 nTPM
Prostate	11.2 nTPM
Skeletal muscle	10.4 nTPM
Stomach	10.1 nTPM
Breast	9.6 nTPM
Fallopian tube	9.3 nTPM
Liver	8.3 nTPM
Pancreas	8.0 nTPM
Adipose tissue	7.9 nTPM
Placenta	7.6 nTPM
Skin	6.6 nTPM

Granulocytes	12.8 nTPM
Tongue	14.6 nTPM
Lung	13.1 nTPM
Fallopian tube	10.6 nTPM

Intestinal goblet cells	4.5 nTPM
Small intestine	4.9 nTPM
Rectum	4.5 nTPM
Colon	3.9 nTPM

Lymphatic endothelial cells	5.6 nTPM
Fallopian tube	11.2 nTPM
Ovary	0.0 nTPM

Macrophages	36.1 nTPM
Adipose tissue	75.8 nTPM
Breast	58.8 nTPM
Esophagus	52.7 nTPM
Tongue	52.0 nTPM
Vascular	41.3 nTPM
Prostate	38.1 nTPM
Skeletal muscle	37.7 nTPM
Fallopian tube	37.2 nTPM
Lung	37.0 nTPM
Endometrium	34.4 nTPM
Stomach	33.4 nTPM
Salivary gland	32.8 nTPM
Spleen	31.1 nTPM
Thymus	29.9 nTPM
Bone marrow	22.3 nTPM
Testis	18.6 nTPM
Pancreas	18.5 nTPM
Kidney	17.7 nTPM
Skin	16.7 nTPM

Basal prostatic cells	12.1 nTPM
Prostate	12.1 nTPM

Bipolar cells	19.5 nTPM
Eye	19.5 nTPM

Collecting duct cells	9.7 nTPM
Kidney	9.7 nTPM

Cone photoreceptor cells	25.5 nTPM
Eye	25.5 nTPM

Paneth cells	9.7 nTPM
Small intestine	17.3 nTPM
Colon	7.2 nTPM
Rectum	4.6 nTPM

Plasma cells	16.3 nTPM
Salivary gland	27.3 nTPM
Bone marrow	19.6 nTPM
Spleen	19.5 nTPM
Thymus	16.6 nTPM
Esophagus	15.6 nTPM
Stomach	15.1 nTPM
Fallopian tube	8.7 nTPM
Liver	8.0 nTPM

Schwann cells	77.8 nTPM
Adipose tissue	112.8 nTPM
Vascular	60.6 nTPM
Esophagus	59.9 nTPM

Serous glandular cells	24.6 nTPM
Salivary gland	27.1 nTPM
Tongue	22.1 nTPM

Smooth muscle cells	13.0 nTPM
Salivary gland	34.9 nTPM
Vascular	24.0 nTPM
Esophagus	19.2 nTPM
Tongue	14.1 nTPM
Fallopian tube	13.0 nTPM
Lung	12.9 nTPM
Skeletal muscle	10.7 nTPM
Thymus	10.7 nTPM
Skin	10.5 nTPM
Endometrium	10.3 nTPM
Ovary	9.7 nTPM
Breast	9.3 nTPM
Prostate	9.1 nTPM
Adipose tissue	8.9 nTPM
Liver	5.5 nTPM
Placenta	5.1 nTPM

Suprabasal keratinocytes	13.6 nTPM
Tongue	17.4 nTPM
Skin	9.8 nTPM

T-cells	16.8 nTPM
Spleen	28.7 nTPM
Esophagus	26.8 nTPM
Lymph node	25.7 nTPM
Vascular	24.9 nTPM
Breast	21.6 nTPM
Stomach	21.5 nTPM
Bone marrow	21.4 nTPM
Colon	17.5 nTPM
Prostate	16.4 nTPM
Adipose tissue	15.8 nTPM
Thymus	15.6 nTPM
Salivary gland	15.5 nTPM
Tongue	15.5 nTPM
Skeletal muscle	15.1 nTPM
Fallopian tube	14.3 nTPM
Endometrium	12.5 nTPM
Lung	11.4 nTPM
Skin	10.5 nTPM
PBMC	10.4 nTPM
Liver	9.4 nTPM
Kidney	2.7 nTPM

Undifferentiated cells	5.9 nTPM
Small intestine	6.9 nTPM
Colon	6.2 nTPM
Rectum	4.6 nTPM

Amygdala excitatory	26.4 nTPM
Hippocampus	29.9 nTPM
Amygdala	28.7 nTPM
Cerebral cortex	26.7 nTPM
Hypothalamus	26.2 nTPM
Basal ganglia	24.6 nTPM
Thalamus	22.2 nTPM

Astrocyte	36.6 nTPM
Amygdala	47.1 nTPM
Hypothalamus	42.8 nTPM
Spinal cord	41.0 nTPM
Hippocampus	36.4 nTPM
Thalamus	36.1 nTPM
Midbrain	35.9 nTPM
Cerebral cortex	35.7 nTPM
Basal ganglia	35.5 nTPM
Pons	32.2 nTPM
Medulla oblongata	31.3 nTPM
Cerebellum	28.6 nTPM

Bergmann glia	42.7 nTPM
Medulla oblongata	51.1 nTPM
Pons	41.7 nTPM
Cerebellum	35.2 nTPM

Central nervous system macrophage	49.3 nTPM
Hypothalamus	60.3 nTPM
Amygdala	54.0 nTPM
Spinal cord	50.3 nTPM
Pons	49.0 nTPM
Basal ganglia	48.4 nTPM
Medulla oblongata	48.4 nTPM
Midbrain	48.4 nTPM
Hippocampus	47.3 nTPM
Cerebellum	47.1 nTPM
Cerebral cortex	44.6 nTPM
Thalamus	44.2 nTPM

Cerebellar inhibitory	25.7 nTPM
Spinal cord	27.5 nTPM
Midbrain	27.4 nTPM
Medulla oblongata	26.7 nTPM
Cerebellum	25.6 nTPM
Pons	21.3 nTPM

Cge interneuron	29.9 nTPM
Hypothalamus	33.9 nTPM
Amygdala	32.9 nTPM
Thalamus	29.7 nTPM
Cerebral cortex	29.0 nTPM
Hippocampus	28.8 nTPM
Basal ganglia	28.5 nTPM
Midbrain	26.5 nTPM

Choroid plexus epithelial cell	35.4 nTPM
Basal ganglia	63.3 nTPM
Medulla oblongata	39.6 nTPM
Hippocampus	22.2 nTPM
Thalamus	16.4 nTPM

Committed oligodendrocyte precursor	52.7 nTPM
Hippocampus	74.0 nTPM
Spinal cord	73.6 nTPM
Cerebral cortex	70.3 nTPM
Midbrain	54.6 nTPM
Amygdala	53.0 nTPM
Pons	50.5 nTPM
Hypothalamus	47.8 nTPM
Basal ganglia	41.6 nTPM
Cerebellum	41.2 nTPM
Medulla oblongata	40.0 nTPM
Thalamus	32.9 nTPM

Deep-layer corticothalamic and 6b	28.8 nTPM
Amygdala	31.1 nTPM
Midbrain	30.0 nTPM
Basal ganglia	29.4 nTPM
Cerebral cortex	28.0 nTPM
Hypothalamus	27.4 nTPM
Hippocampus	26.8 nTPM

Deep-layer intratelencephalic	25.0 nTPM
Amygdala	26.4 nTPM
Hypothalamus	25.2 nTPM
Cerebral cortex	24.8 nTPM
Basal ganglia	24.4 nTPM
Hippocampus	24.2 nTPM

Deep-layer near-projecting	23.0 nTPM
Hypothalamus	28.5 nTPM
Cerebral cortex	23.2 nTPM
Basal ganglia	23.0 nTPM
Amygdala	21.8 nTPM
Hippocampus	18.5 nTPM

Eccentric medium spiny neuron	29.1 nTPM
Amygdala	33.2 nTPM
Cerebral cortex	31.1 nTPM
Hypothalamus	30.3 nTPM
Hippocampus	29.8 nTPM
Basal ganglia	25.3 nTPM
Thalamus	24.6 nTPM