Single cell type - LAMP2 - The Human Protein Atlas

LAMP2

Search result

Field

Term

Cluster

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.	LAMP2
Gene descriptionⁱ Full gene name according to HGNC.	Lysosomal associated membrane protein 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	CD markers Disease related genes Human disease related genes Plasma proteins Potential drug targets 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	Macrophages - 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 (Syncytiotrophoblasts, 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.	0.31
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.	Cell type enhanced (Oligodendrocyte)
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.	Immune cell enhanced (neutrophil)
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 (Syncytiotrophoblasts, 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: Cell type enhanced (Oligodendrocyte)

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: Immune cell enhanced (neutrophil)
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

LAMP2 is part of cluster 58 Macrophages - Innate immune response with confidenceⁱ 1
420 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.
SLC31A1	Solute carrier family 31 member 1	0.6617	58
SCARB2	Scavenger receptor class B member 2	0.5942	58
ATP6AP1	ATPase H+ transporting accessory protein 1	0.5934	58
OS9	OS9 endoplasmic reticulum lectin	0.5413	77
SLC31A2	Solute carrier family 31 member 2	0.5404	75
GRN	Granulin precursor	0.5306	58
HEXA	Hexosaminidase subunit alpha	0.5279	58
NCSTN	Nicastrin	0.5265	58
DNASE2B	Deoxyribonuclease 2 beta	0.5236	75
RRAGD	Ras related GTP binding D	0.5220	75
ITM2B	Integral membrane protein 2B	0.5138	80
TLR5	Toll like receptor 5	0.5089	58
H6PD	Hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase	0.5080	75
MAGT1	Magnesium transporter 1	0.5056	77
TCN1	Transcobalamin 1	0.5049	75

IMMUNE CELLS

LAMP2 is part of cluster 7 Non-specific - Innate immune response with confidenceⁱ 1
237 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.
RHOG	Ras homolog family member G	1.0000	7
RAB11FIP1	RAB11 family interacting protein 1	1.0000	7
VSIR	V-set immunoregulatory receptor	1.0000	7
NINJ1	Ninjurin 1	1.0000	7
SMNDC1	Survival motor neuron domain containing 1	0.9762	7
HLA-B	Major histocompatibility complex, class I, B	0.9762	7
RASGRP4	RAS guanyl releasing protein 4	0.9762	7
SHISA5	Shisa family member 5	0.9762	7
SLA	Src like adaptor	0.9762	7
PAK1	P21 (RAC1) activated kinase 1	0.9762	7
IMPA2	Inositol monophosphatase 2	0.9762	7
NADK	NAD kinase	0.9762	7
HPCAL1	Hippocalcin like 1	0.9762	7
STX10	Syntaxin 10	0.9762	7
MAEA	Macrophage erythroblast attacher, E3 ubiquitin ligase	0.9762	7

Adipocytes	76.2 nTPM
Adipose tissue	92.7 nTPM
Breast	59.7 nTPM

Alveolar cells type 1	72.5 nTPM
Lung	72.5 nTPM

Alveolar cells type 2	64.8 nTPM
Lung	64.8 nTPM

Astrocytes	49.5 nTPM
Brain	49.5 nTPM

B-cells	29.1 nTPM
Skin	52.5 nTPM
Adipose tissue	47.3 nTPM
Salivary gland	38.7 nTPM
Stomach	32.9 nTPM
PBMC	30.8 nTPM
Lung	29.5 nTPM
Bone marrow	25.2 nTPM
Thymus	24.8 nTPM
Liver	24.2 nTPM
Kidney	20.8 nTPM
Spleen	20.8 nTPM
Lymph node	18.7 nTPM
Esophagus	11.8 nTPM

Ciliated cells	80.9 nTPM
Endometrium	101.6 nTPM
Bronchus	98.9 nTPM
Fallopian tube	69.7 nTPM
Lung	53.5 nTPM

Club cells	134.7 nTPM
Bronchus	242.4 nTPM
Lung	92.9 nTPM
Prostate	68.8 nTPM

Dendritic cells	65.9 nTPM
Adipose tissue	77.9 nTPM
PBMC	54.0 nTPM

Endothelial cells	73.1 nTPM
Pancreas	103.4 nTPM
Liver	95.7 nTPM
Heart muscle	94.3 nTPM
Salivary gland	82.4 nTPM
Tongue	81.7 nTPM
Lung	81.1 nTPM
Placenta	77.2 nTPM
Breast	72.9 nTPM
Endometrium	72.2 nTPM
Skeletal muscle	70.6 nTPM
Skin	69.6 nTPM
Prostate	66.3 nTPM
Testis	64.4 nTPM
Vascular	61.5 nTPM
Thymus	58.9 nTPM
Fallopian tube	57.2 nTPM
Esophagus	56.1 nTPM
Ovary	50.3 nTPM

Enteroendocrine cells	41.0 nTPM
Rectum	48.6 nTPM
Small intestine	37.8 nTPM
Colon	36.5 nTPM

Fibroblasts	119.8 nTPM
Adipose tissue	179.1 nTPM
Fallopian tube	166.4 nTPM
Heart muscle	149.8 nTPM
Liver	147.1 nTPM
Skeletal muscle	142.5 nTPM
Stomach	135.5 nTPM
Salivary gland	128.7 nTPM
Esophagus	123.1 nTPM
Prostate	112.2 nTPM
Vascular	110.6 nTPM
Skin	109.5 nTPM
Pancreas	106.9 nTPM
Breast	88.4 nTPM
Thymus	85.5 nTPM
Lung	71.5 nTPM
Placenta	60.5 nTPM

Granulocytes	34.2 nTPM
Fallopian tube	34.4 nTPM
Lung	34.3 nTPM
Tongue	34.0 nTPM

Intestinal goblet cells	39.0 nTPM
Small intestine	45.0 nTPM
Rectum	40.7 nTPM
Colon	31.2 nTPM

Lymphatic endothelial cells	80.1 nTPM
Fallopian tube	94.7 nTPM
Ovary	65.5 nTPM

Macrophages	154.9 nTPM
Lung	353.1 nTPM
Vascular	204.1 nTPM
Skin	196.1 nTPM
Esophagus	195.2 nTPM
Pancreas	191.2 nTPM
Fallopian tube	177.4 nTPM
Spleen	174.4 nTPM
Adipose tissue	170.6 nTPM
Salivary gland	158.0 nTPM
Prostate	136.5 nTPM
Thymus	128.9 nTPM
Stomach	126.0 nTPM
Kidney	123.0 nTPM
Skeletal muscle	121.7 nTPM
Tongue	117.7 nTPM
Bone marrow	113.5 nTPM
Testis	89.3 nTPM
Endometrium	86.1 nTPM
Breast	81.0 nTPM

Basal keratinocytes	114.0 nTPM
Skin	114.2 nTPM
Tongue	113.8 nTPM

Basal respiratory cells	253.1 nTPM
Bronchus	253.1 nTPM

Cholangiocytes	194.6 nTPM
Liver	194.6 nTPM

Collecting duct cells	68.1 nTPM
Kidney	68.1 nTPM

Paneth cells	49.5 nTPM
Small intestine	76.0 nTPM
Rectum	50.8 nTPM
Colon	21.7 nTPM

Plasma cells	91.3 nTPM
Fallopian tube	229.0 nTPM
Salivary gland	144.2 nTPM
Stomach	129.8 nTPM
Esophagus	67.6 nTPM
Liver	60.6 nTPM
Thymus	41.6 nTPM
Spleen	33.2 nTPM
Bone marrow	24.2 nTPM

Schwann cells	113.6 nTPM
Vascular	188.6 nTPM
Esophagus	107.8 nTPM
Adipose tissue	44.5 nTPM

Serous glandular cells	220.8 nTPM
Salivary gland	300.2 nTPM
Tongue	141.4 nTPM

Smooth muscle cells	62.1 nTPM
Salivary gland	109.3 nTPM
Placenta	103.6 nTPM
Tongue	91.6 nTPM
Lung	75.2 nTPM
Adipose tissue	74.6 nTPM
Liver	70.0 nTPM
Endometrium	58.8 nTPM
Fallopian tube	56.3 nTPM
Prostate	56.0 nTPM
Vascular	56.0 nTPM
Skeletal muscle	52.9 nTPM
Skin	51.4 nTPM
Ovary	41.9 nTPM
Thymus	36.8 nTPM
Breast	34.8 nTPM
Esophagus	24.0 nTPM

Suprabasal keratinocytes	161.1 nTPM
Tongue	181.8 nTPM
Skin	140.4 nTPM

T-cells	35.3 nTPM
Prostate	50.9 nTPM
Fallopian tube	50.1 nTPM
Tongue	50.0 nTPM
Adipose tissue	45.2 nTPM
Kidney	43.4 nTPM
Salivary gland	42.7 nTPM
Skeletal muscle	42.3 nTPM
PBMC	40.3 nTPM
Lung	40.0 nTPM
Endometrium	35.2 nTPM
Skin	33.3 nTPM
Stomach	31.8 nTPM
Thymus	31.4 nTPM
Bone marrow	30.0 nTPM
Liver	29.1 nTPM
Spleen	28.6 nTPM
Breast	27.2 nTPM
Vascular	26.5 nTPM
Lymph node	25.5 nTPM
Esophagus	21.9 nTPM
Colon	16.6 nTPM

Undifferentiated cells	33.4 nTPM
Rectum	36.2 nTPM
Small intestine	34.1 nTPM
Colon	30.0 nTPM

Amygdala excitatory	43.2 nTPM
Thalamus	47.6 nTPM
Basal ganglia	46.1 nTPM
Hippocampus	44.3 nTPM
Hypothalamus	41.2 nTPM
Cerebral cortex	40.7 nTPM
Amygdala	39.3 nTPM

Astrocyte	120.7 nTPM
Spinal cord	154.5 nTPM
Cerebellum	143.1 nTPM
Midbrain	134.6 nTPM
Pons	121.0 nTPM
Thalamus	120.4 nTPM
Medulla oblongata	119.6 nTPM
Basal ganglia	114.7 nTPM
Amygdala	109.7 nTPM
Cerebral cortex	105.1 nTPM
Hypothalamus	104.6 nTPM
Hippocampus	100.2 nTPM

Bergmann glia	68.9 nTPM
Medulla oblongata	70.3 nTPM
Cerebellum	70.1 nTPM
Pons	66.2 nTPM

Central nervous system macrophage	99.3 nTPM
Spinal cord	127.5 nTPM
Midbrain	112.8 nTPM
Basal ganglia	106.0 nTPM
Thalamus	104.8 nTPM
Amygdala	99.1 nTPM
Cerebellum	99.0 nTPM
Pons	96.7 nTPM
Hippocampus	94.6 nTPM
Cerebral cortex	87.6 nTPM
Hypothalamus	86.3 nTPM
Medulla oblongata	77.4 nTPM

Cerebellar inhibitory	48.2 nTPM
Pons	51.0 nTPM
Medulla oblongata	49.0 nTPM
Cerebellum	47.8 nTPM
Midbrain	46.7 nTPM
Spinal cord	46.7 nTPM

Cge interneuron	52.5 nTPM
Thalamus	61.2 nTPM
Midbrain	56.3 nTPM
Basal ganglia	51.5 nTPM
Cerebral cortex	51.3 nTPM
Amygdala	50.9 nTPM
Hypothalamus	48.4 nTPM
Hippocampus	47.8 nTPM

Choroid plexus epithelial cell	52.9 nTPM
Thalamus	93.2 nTPM
Basal ganglia	53.0 nTPM
Medulla oblongata	34.9 nTPM
Hippocampus	30.5 nTPM

Committed oligodendrocyte precursor	218.2 nTPM
Thalamus	458.1 nTPM
Hypothalamus	368.0 nTPM
Amygdala	338.9 nTPM
Basal ganglia	274.3 nTPM
Cerebral cortex	192.5 nTPM
Midbrain	178.1 nTPM
Hippocampus	174.1 nTPM
Pons	142.5 nTPM
Spinal cord	103.0 nTPM
Cerebellum	96.7 nTPM
Medulla oblongata	73.6 nTPM

Deep-layer corticothalamic and 6b	42.0 nTPM
Amygdala	50.3 nTPM
Hippocampus	46.1 nTPM
Cerebral cortex	42.6 nTPM
Basal ganglia	39.7 nTPM
Hypothalamus	37.9 nTPM
Midbrain	35.5 nTPM

Deep-layer intratelencephalic	42.4 nTPM
Hippocampus	46.5 nTPM
Amygdala	44.7 nTPM
Hypothalamus	42.1 nTPM
Cerebral cortex	40.7 nTPM
Basal ganglia	37.8 nTPM

Deep-layer near-projecting	39.1 nTPM
Cerebral cortex	42.5 nTPM
Basal ganglia	41.6 nTPM
Hypothalamus	39.2 nTPM
Amygdala	39.1 nTPM
Hippocampus	33.2 nTPM

Eccentric medium spiny neuron	47.5 nTPM
Thalamus	50.6 nTPM
Amygdala	49.9 nTPM
Hypothalamus	49.1 nTPM
Cerebral cortex	46.8 nTPM
Hippocampus	45.2 nTPM
Basal ganglia	43.2 nTPM