Single cell type - LY6H - The Human Protein Atlas

LY6H

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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.	LY6H
Gene descriptionⁱ Full gene name according to HGNC.	Lymphocyte antigen 6 family member H
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	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.	Neurons - Neuronal signaling (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 (Inhibitory neurons, Spermatogonia, Excitatory neurons, Adipocytes, Oligodendrocyte precursor cells, Enteroendocrine cells, Horizontal 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.	0.84
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.	Not detected in immune cells
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 (Inhibitory neurons, Spermatogonia, Excitatory neurons, Adipocytes, Oligodendrocyte precursor cells, Enteroendocrine cells, Horizontal 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: Not detected in immune cells
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

LY6H is part of cluster 69 Neurons - Neuronal signaling with confidenceⁱ 1
331 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.
NYAP1	Neuronal tyrosine phosphorylated phosphoinositide-3-kinase adaptor 1	0.7042	10
ANKRD30BL	Ankyrin repeat domain 30B like	0.6684	69
CACNG8	Calcium voltage-gated channel auxiliary subunit gamma 8	0.6659	69
C8orf34	Chromosome 8 open reading frame 34	0.6648	69
CHRFAM7A	CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion	0.6491	69
RTN1	Reticulon 1	0.6483	69
MYT1L	Myelin transcription factor 1 like	0.6473	69
FRMPD3	FERM and PDZ domain containing 3	0.6339	69
KCNT2	Potassium sodium-activated channel subfamily T member 2	0.6320	69
HTR1E	5-hydroxytryptamine receptor 1E	0.6187	69
GPR12	G protein-coupled receptor 12	0.6159	71
MYRIP	Myosin VIIA and Rab interacting protein	0.6150	69
PIANP	PILR alpha associated neural protein	0.6105	71
CAMKV	CaM kinase like vesicle associated	0.6103	69
SYNGR3	Synaptogyrin 3	0.6052	69

Adipocytes	22.0 nTPM
Adipose tissue	42.1 nTPM
Breast	1.9 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	8.7 nTPM
Brain	8.7 nTPM

B-cells	0.0 nTPM
Stomach	0.4 nTPM
Thymus	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM

Ciliated cells	8.2 nTPM
Lung	19.4 nTPM
Fallopian tube	8.8 nTPM
Bronchus	3.4 nTPM
Endometrium	1.0 nTPM

Club cells	1.1 nTPM
Lung	1.6 nTPM
Prostate	1.2 nTPM
Bronchus	0.5 nTPM

Endothelial cells	5.2 nTPM
Ovary	43.2 nTPM
Salivary gland	14.3 nTPM
Pancreas	10.3 nTPM
Tongue	5.4 nTPM
Skeletal muscle	5.2 nTPM
Placenta	4.0 nTPM
Lung	4.0 nTPM
Fallopian tube	1.8 nTPM
Liver	1.3 nTPM
Breast	0.9 nTPM
Vascular	0.8 nTPM
Endometrium	0.7 nTPM
Testis	0.3 nTPM
Prostate	0.2 nTPM
Thymus	0.2 nTPM
Skin	0.1 nTPM
Heart muscle	0.0 nTPM
Esophagus	0.0 nTPM

Enteroendocrine cells	18.1 nTPM
Rectum	35.2 nTPM
Small intestine	17.2 nTPM
Colon	1.8 nTPM

Fibroblasts	2.6 nTPM
Esophagus	32.3 nTPM
Placenta	3.0 nTPM
Stomach	2.9 nTPM
Prostate	2.6 nTPM
Breast	0.4 nTPM
Fallopian tube	0.3 nTPM
Skeletal muscle	0.2 nTPM
Pancreas	0.1 nTPM
Vascular	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.4 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.3 nTPM
Small intestine	0.7 nTPM
Rectum	0.3 nTPM
Colon	0.0 nTPM

Lymphatic endothelial cells	1.4 nTPM
Fallopian tube	2.9 nTPM
Ovary	0.0 nTPM

Macrophages	0.1 nTPM
Esophagus	1.3 nTPM
Testis	0.6 nTPM
Salivary gland	0.3 nTPM
Fallopian tube	0.1 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM

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

Bipolar cells	2.0 nTPM
Eye	2.0 nTPM

Early spermatids	1.5 nTPM
Testis	1.5 nTPM

Plasma cells	0.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

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

Smooth muscle cells	0.2 nTPM
Placenta	2.2 nTPM
Liver	0.4 nTPM
Ovary	0.4 nTPM
Skeletal muscle	0.2 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

T-cells	0.1 nTPM
Tongue	0.3 nTPM
Prostate	0.2 nTPM
Breast	0.2 nTPM
Endometrium	0.1 nTPM
Adipose tissue	0.1 nTPM
Stomach	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.2 nTPM
Rectum	0.5 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Amygdala excitatory	126.5 nTPM
Thalamus	194.2 nTPM
Basal ganglia	176.1 nTPM
Hypothalamus	105.5 nTPM
Amygdala	96.4 nTPM
Hippocampus	94.2 nTPM
Cerebral cortex	92.8 nTPM

Astrocyte	8.6 nTPM
Hypothalamus	18.3 nTPM
Medulla oblongata	12.4 nTPM
Cerebral cortex	12.1 nTPM
Hippocampus	10.1 nTPM
Thalamus	8.7 nTPM
Amygdala	8.0 nTPM
Midbrain	6.6 nTPM
Spinal cord	6.4 nTPM
Basal ganglia	6.2 nTPM
Pons	3.9 nTPM
Cerebellum	2.3 nTPM

Bergmann glia	3.5 nTPM
Medulla oblongata	8.5 nTPM
Pons	1.4 nTPM
Cerebellum	0.4 nTPM

Central nervous system macrophage	10.1 nTPM
Hypothalamus	26.1 nTPM
Cerebral cortex	23.0 nTPM
Hippocampus	19.0 nTPM
Amygdala	13.0 nTPM
Thalamus	9.4 nTPM
Medulla oblongata	5.4 nTPM
Midbrain	4.9 nTPM
Basal ganglia	3.6 nTPM
Pons	3.5 nTPM
Spinal cord	2.1 nTPM
Cerebellum	0.9 nTPM

Cerebellar inhibitory	18.2 nTPM
Pons	30.0 nTPM
Midbrain	26.1 nTPM
Spinal cord	16.5 nTPM
Medulla oblongata	11.8 nTPM
Cerebellum	6.6 nTPM

Cge interneuron	162.3 nTPM
Basal ganglia	212.6 nTPM
Midbrain	191.3 nTPM
Hippocampus	165.4 nTPM
Amygdala	163.0 nTPM
Thalamus	151.5 nTPM
Cerebral cortex	147.6 nTPM
Hypothalamus	105.0 nTPM

Choroid plexus epithelial cell	4.8 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	4.1 nTPM
Thalamus	2.7 nTPM
Basal ganglia	1.3 nTPM

Committed oligodendrocyte precursor	24.4 nTPM
Cerebral cortex	46.9 nTPM
Midbrain	37.0 nTPM
Hypothalamus	35.5 nTPM
Medulla oblongata	27.1 nTPM
Basal ganglia	26.8 nTPM
Amygdala	25.9 nTPM
Hippocampus	22.2 nTPM
Pons	17.7 nTPM
Thalamus	15.1 nTPM
Spinal cord	11.0 nTPM
Cerebellum	3.2 nTPM

Deep-layer corticothalamic and 6b	161.5 nTPM
Basal ganglia	206.9 nTPM
Midbrain	200.8 nTPM
Amygdala	176.1 nTPM
Cerebral cortex	149.7 nTPM
Hippocampus	127.9 nTPM
Hypothalamus	107.6 nTPM

Deep-layer intratelencephalic	125.4 nTPM
Basal ganglia	155.0 nTPM
Amygdala	152.2 nTPM
Hippocampus	129.1 nTPM
Cerebral cortex	102.1 nTPM
Hypothalamus	88.7 nTPM

Deep-layer near-projecting	100.2 nTPM
Hippocampus	143.8 nTPM
Basal ganglia	139.4 nTPM
Amygdala	74.8 nTPM
Cerebral cortex	72.8 nTPM
Hypothalamus	70.0 nTPM

Eccentric medium spiny neuron	146.1 nTPM
Amygdala	181.5 nTPM
Hippocampus	178.7 nTPM
Hypothalamus	156.9 nTPM
Thalamus	140.0 nTPM
Cerebral cortex	128.5 nTPM
Basal ganglia	91.2 nTPM

Endothelial cell	7.3 nTPM
Amygdala	15.6 nTPM
Hippocampus	11.9 nTPM
Hypothalamus	9.9 nTPM
Cerebral cortex	9.6 nTPM
Midbrain	7.6 nTPM
Spinal cord	6.9 nTPM
Basal ganglia	6.5 nTPM
Thalamus	6.2 nTPM
Medulla oblongata	5.1 nTPM
Pons	1.2 nTPM
Cerebellum	0.0 nTPM

Ependymal cell	34.2 nTPM
Spinal cord	57.5 nTPM
Medulla oblongata	41.9 nTPM
Hippocampus	36.9 nTPM
Thalamus	36.4 nTPM
Hypothalamus	31.2 nTPM
Basal ganglia	30.7 nTPM
Midbrain	29.8 nTPM
Pons	25.1 nTPM
Amygdala	18.2 nTPM