Single cell type - LYN - The Human Protein Atlas

LYN

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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.	LYN
Gene descriptionⁱ Full gene name according to HGNC.	LYN proto-oncogene, Src family tyrosine kinase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Enzymes Potential drug targets
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.	3

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, B-cells, Macrophages)
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.	0.60
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.	Group enriched (Central nervous system macrophage, Leukocyte)
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 (Monocytes, B-cells, Macrophages)

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: Group enriched (Central nervous system macrophage, Leukocyte)

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

LYN is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 1
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.
FCAR	Fc alpha receptor	0.7365	29
MEFV	MEFV innate immuity regulator, pyrin	0.7258	29
SCIMP	SLP adaptor and CSK interacting membrane protein	0.7224	73
ATG16L2	Autophagy related 16 like 2	0.7206	74
POU2F2	POU class 2 homeobox 2	0.7073	73
CD1D	CD1d molecule	0.7053	29
CD300H	CD300H molecule (gene/pseudogene)	0.7037	29
ADGRE2	Adhesion G protein-coupled receptor E2	0.7002	29
PTPN6	Protein tyrosine phosphatase non-receptor type 6	0.6858	73
DOK3	Docking protein 3	0.6782	74
GAPT	GRB2 binding adaptor protein, transmembrane	0.6657	28
C19orf38	Chromosome 19 open reading frame 38	0.6641	29
LILRA2	Leukocyte immunoglobulin like receptor A2	0.6593	29
LILRA5	Leukocyte immunoglobulin like receptor A5	0.6577	29
LAT2	Linker for activation of T cells family member 2	0.6513	73

IMMUNE CELLS

LYN is part of cluster 37 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 0.6
275 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.
LBX2	Ladybird homeobox 2	1.0000	37
ASH2L	ASH2 like, histone lysine methyltransferase complex subunit	1.0000	37
BID	BH3 interacting domain death agonist	0.9762	37
TRIQK	Triple QxxK/R motif containing	0.9762	37
LST1	Leukocyte specific transcript 1	0.9762	37
PTP4A3	Protein tyrosine phosphatase 4A3	0.9762	37
P2RX1	Purinergic receptor P2X 1	0.9762	37
ZFAND5	Zinc finger AN1-type containing 5	0.9762	37
TCIRG1	T cell immune regulator 1, ATPase H+ transporting V0 subunit a3	0.9524	37
ERGIC1	Endoplasmic reticulum-golgi intermediate compartment 1	0.9524	37
PFKFB4	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	0.9524	37
LILRA1	Leukocyte immunoglobulin like receptor A1	0.9524	37
RABGAP1L	RAB GTPase activating protein 1 like	0.9524	37
CHST2	Carbohydrate sulfotransferase 2	0.9524	37
CMTM6	CKLF like MARVEL transmembrane domain containing 6	0.9524	37

Adipocytes	19.7 nTPM
Breast	19.8 nTPM
Adipose tissue	19.6 nTPM

Alveolar cells type 1	61.0 nTPM
Lung	61.0 nTPM

Alveolar cells type 2	73.4 nTPM
Lung	73.4 nTPM

Astrocytes	26.3 nTPM
Brain	26.3 nTPM

B-cells	208.2 nTPM
Lymph node	392.6 nTPM
Stomach	342.5 nTPM
Adipose tissue	326.3 nTPM
Spleen	305.5 nTPM
Bone marrow	240.4 nTPM
Esophagus	200.6 nTPM
Thymus	180.6 nTPM
Salivary gland	163.9 nTPM
Lung	154.3 nTPM
PBMC	140.1 nTPM
Liver	115.9 nTPM
Kidney	78.0 nTPM
Skin	66.1 nTPM

Ciliated cells	29.7 nTPM
Bronchus	56.5 nTPM
Lung	30.9 nTPM
Fallopian tube	17.0 nTPM
Endometrium	14.3 nTPM

Club cells	41.1 nTPM
Lung	56.2 nTPM
Bronchus	51.2 nTPM
Prostate	15.9 nTPM

Dendritic cells	160.1 nTPM
PBMC	179.9 nTPM
Adipose tissue	140.4 nTPM

Endothelial cells	23.8 nTPM
Breast	66.8 nTPM
Pancreas	33.6 nTPM
Salivary gland	32.5 nTPM
Esophagus	30.7 nTPM
Liver	29.0 nTPM
Endometrium	25.5 nTPM
Lung	25.2 nTPM
Fallopian tube	24.9 nTPM
Tongue	23.5 nTPM
Vascular	22.6 nTPM
Placenta	21.6 nTPM
Skin	20.6 nTPM
Thymus	20.4 nTPM
Prostate	17.6 nTPM
Skeletal muscle	15.2 nTPM
Testis	6.7 nTPM
Heart muscle	6.3 nTPM
Ovary	5.1 nTPM

Enteroendocrine cells	4.6 nTPM
Colon	10.6 nTPM
Rectum	3.4 nTPM
Small intestine	0.0 nTPM

Fibroblasts	9.3 nTPM
Liver	34.4 nTPM
Stomach	15.9 nTPM
Lung	12.6 nTPM
Fallopian tube	10.4 nTPM
Heart muscle	9.7 nTPM
Thymus	8.4 nTPM
Prostate	7.9 nTPM
Salivary gland	7.3 nTPM
Esophagus	7.0 nTPM
Skin	6.9 nTPM
Pancreas	6.8 nTPM
Vascular	6.2 nTPM
Placenta	5.4 nTPM
Skeletal muscle	5.3 nTPM
Adipose tissue	3.2 nTPM
Breast	1.0 nTPM

Granulocytes	76.5 nTPM
Lung	110.9 nTPM
Tongue	63.1 nTPM
Fallopian tube	55.5 nTPM

Intestinal goblet cells	13.3 nTPM
Small intestine	19.2 nTPM
Rectum	11.2 nTPM
Colon	9.3 nTPM

Lymphatic endothelial cells	78.5 nTPM
Fallopian tube	124.4 nTPM
Ovary	32.7 nTPM

Macrophages	206.2 nTPM
Spleen	447.1 nTPM
Bone marrow	430.7 nTPM
Stomach	349.8 nTPM
Fallopian tube	345.5 nTPM
Skeletal muscle	277.8 nTPM
Kidney	199.1 nTPM
Adipose tissue	185.8 nTPM
Lung	183.2 nTPM
Endometrium	155.6 nTPM
Thymus	153.4 nTPM
Salivary gland	146.3 nTPM
Prostate	142.2 nTPM
Tongue	140.3 nTPM
Esophagus	140.0 nTPM
Testis	138.2 nTPM
Vascular	130.8 nTPM
Breast	124.3 nTPM
Pancreas	117.2 nTPM
Skin	110.3 nTPM

Basal keratinocytes	4.5 nTPM
Tongue	5.6 nTPM
Skin	3.3 nTPM

Basal prostatic cells	14.1 nTPM
Prostate	14.1 nTPM

Basal respiratory cells	40.2 nTPM
Bronchus	40.2 nTPM

Basal squamous epithelial cells	6.4 nTPM
Esophagus	6.4 nTPM

Paneth cells	13.0 nTPM
Colon	14.5 nTPM
Rectum	14.1 nTPM
Small intestine	10.4 nTPM

Plasma cells	48.7 nTPM
Spleen	86.8 nTPM
Bone marrow	57.4 nTPM
Thymus	56.8 nTPM
Stomach	49.4 nTPM
Esophagus	46.8 nTPM
Salivary gland	38.1 nTPM
Liver	32.0 nTPM
Fallopian tube	22.2 nTPM

Schwann cells	68.2 nTPM
Adipose tissue	203.0 nTPM
Vascular	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	34.8 nTPM
Salivary gland	38.7 nTPM
Tongue	30.9 nTPM

Smooth muscle cells	9.7 nTPM
Placenta	47.6 nTPM
Liver	11.5 nTPM
Lung	10.6 nTPM
Endometrium	9.4 nTPM
Thymus	9.4 nTPM
Salivary gland	8.6 nTPM
Prostate	7.9 nTPM
Tongue	7.8 nTPM
Skeletal muscle	7.4 nTPM
Skin	7.0 nTPM
Ovary	6.9 nTPM
Vascular	6.5 nTPM
Esophagus	4.8 nTPM
Fallopian tube	4.3 nTPM
Breast	2.9 nTPM
Adipose tissue	2.7 nTPM

T-cells	19.8 nTPM
Colon	53.6 nTPM
Liver	39.3 nTPM
Skeletal muscle	37.0 nTPM
Bone marrow	35.7 nTPM
Endometrium	31.3 nTPM
Spleen	27.2 nTPM
Stomach	26.2 nTPM
Vascular	23.7 nTPM
Fallopian tube	22.4 nTPM
Lung	18.9 nTPM
Prostate	15.2 nTPM
Adipose tissue	12.8 nTPM
Kidney	11.5 nTPM
Breast	11.2 nTPM
Esophagus	9.7 nTPM
Salivary gland	9.0 nTPM
Skin	8.4 nTPM
PBMC	8.1 nTPM
Lymph node	6.5 nTPM
Tongue	4.5 nTPM
Thymus	2.5 nTPM

Undifferentiated cells	16.6 nTPM
Small intestine	24.3 nTPM
Rectum	13.1 nTPM
Colon	12.3 nTPM

Amygdala excitatory	1.7 nTPM
Thalamus	2.7 nTPM
Hypothalamus	1.9 nTPM
Amygdala	1.6 nTPM
Cerebral cortex	1.4 nTPM
Basal ganglia	1.3 nTPM
Hippocampus	1.2 nTPM

Astrocyte	19.6 nTPM
Cerebral cortex	69.8 nTPM
Hippocampus	66.3 nTPM
Hypothalamus	25.1 nTPM
Amygdala	19.5 nTPM
Basal ganglia	13.3 nTPM
Spinal cord	8.3 nTPM
Medulla oblongata	5.8 nTPM
Midbrain	2.4 nTPM
Cerebellum	2.0 nTPM
Pons	1.7 nTPM
Thalamus	1.7 nTPM

Bergmann glia	7.2 nTPM
Cerebellum	8.0 nTPM
Pons	7.2 nTPM
Medulla oblongata	6.4 nTPM

Central nervous system macrophage	650.5 nTPM
Hypothalamus	783.9 nTPM
Amygdala	775.7 nTPM
Hippocampus	663.7 nTPM
Midbrain	659.1 nTPM
Basal ganglia	655.1 nTPM
Cerebellum	629.7 nTPM
Cerebral cortex	621.5 nTPM
Thalamus	609.7 nTPM
Pons	606.5 nTPM
Spinal cord	598.8 nTPM
Medulla oblongata	551.6 nTPM

Cerebellar inhibitory	4.5 nTPM
Spinal cord	11.0 nTPM
Midbrain	3.7 nTPM
Medulla oblongata	3.1 nTPM
Cerebellum	2.9 nTPM
Pons	2.0 nTPM

Cge interneuron	1.8 nTPM
Hypothalamus	2.1 nTPM
Amygdala	2.0 nTPM
Basal ganglia	1.8 nTPM
Midbrain	1.8 nTPM
Thalamus	1.8 nTPM
Hippocampus	1.5 nTPM
Cerebral cortex	1.4 nTPM

Choroid plexus epithelial cell	80.6 nTPM
Basal ganglia	136.0 nTPM
Medulla oblongata	92.8 nTPM
Thalamus	49.3 nTPM
Hippocampus	44.4 nTPM

Committed oligodendrocyte precursor	9.7 nTPM
Medulla oblongata	32.3 nTPM
Basal ganglia	19.2 nTPM
Cerebral cortex	10.8 nTPM
Hippocampus	9.6 nTPM
Cerebellum	7.9 nTPM
Pons	6.2 nTPM
Hypothalamus	5.5 nTPM
Amygdala	5.1 nTPM
Thalamus	4.3 nTPM
Spinal cord	3.7 nTPM
Midbrain	2.5 nTPM

Deep-layer corticothalamic and 6b	1.7 nTPM
Hypothalamus	4.5 nTPM
Amygdala	1.5 nTPM
Basal ganglia	1.4 nTPM
Hippocampus	1.4 nTPM
Cerebral cortex	1.2 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	1.5 nTPM
Hypothalamus	2.0 nTPM
Amygdala	1.6 nTPM
Hippocampus	1.4 nTPM
Basal ganglia	1.3 nTPM
Cerebral cortex	1.3 nTPM

Deep-layer near-projecting	1.1 nTPM
Hippocampus	1.6 nTPM
Hypothalamus	1.5 nTPM
Basal ganglia	1.1 nTPM
Cerebral cortex	1.1 nTPM
Amygdala	0.2 nTPM

Eccentric medium spiny neuron	1.2 nTPM
Amygdala	1.5 nTPM
Basal ganglia	1.3 nTPM
Thalamus	1.3 nTPM
Cerebral cortex	1.2 nTPM
Hypothalamus	1.0 nTPM
Hippocampus	0.8 nTPM

Endothelial cell	41.8 nTPM
Basal ganglia	68.0 nTPM
Hypothalamus	54.6 nTPM
Cerebellum	52.7 nTPM
Pons	46.2 nTPM
Thalamus	42.9 nTPM
Amygdala	42.5 nTPM
Hippocampus	38.8 nTPM
Medulla oblongata	34.9 nTPM
Midbrain	33.1 nTPM
Cerebral cortex	25.6 nTPM
Spinal cord	20.7 nTPM