Single cell type - GP6 - The Human Protein Atlas

GP6

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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.	GP6
Gene descriptionⁱ Full gene name according to HGNC.	Glycoprotein VI platelet
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.	Membrane, 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.	Platelets - Hemostasis (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 (Early spermatids, Late spermatids, Inhibitory neurons, Excitatory neurons, 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 (Early spermatids, Late spermatids, Inhibitory neurons, Excitatory neurons, 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

GP6 is part of cluster 57 Platelets - Hemostasis with confidenceⁱ 1
173 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.
PPBP	Pro-platelet basic protein	0.7811	57
GP9	Glycoprotein IX platelet	0.7810	57
PF4	Platelet factor 4	0.7801	57
TUBB1	Tubulin beta 1 class VI	0.7799	57
TREML1	Triggering receptor expressed on myeloid cells like 1	0.7793	57
NRGN	Neurogranin	0.7782	57
LY6G6F	Lymphocyte antigen 6 family member G6F	0.7782	57
RGS18	Regulator of G protein signaling 18	0.7777	57
ITGA2B	Integrin subunit alpha 2b	0.7772	57
RUFY1	RUN and FYVE domain containing 1	0.7723	57
GP1BA	Glycoprotein Ib platelet subunit alpha	0.7694	57
FERMT3	FERM domain containing kindlin 3	0.7662	57
MPIG6B	Megakaryocyte and platelet inhibitory receptor G6b	0.7660	57
ZGLP1	Zinc finger GATA like protein 1	0.7597	57
H3C10	H3 clustered histone 10	0.7587	57

IMMUNE CELLS

GP6 is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.99
504 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.
LBR	Lamin B receptor	1.0000	35
RAF1	Raf-1 proto-oncogene, serine/threonine kinase	0.9762	35
ARID3B	AT-rich interaction domain 3B	0.9762	35
C11orf68	Chromosome 11 open reading frame 68	0.9762	35
CXCR1	C-X-C motif chemokine receptor 1	0.9762	35
RASSF3	Ras association domain family member 3	0.9762	4
BCAS3	BCAS3 microtubule associated cell migration factor	0.9762	4
GRTP1	Growth hormone regulated TBC protein 1	0.9762	35
NIBAN1	Niban apoptosis regulator 1	0.9762	35
USP15	Ubiquitin specific peptidase 15	0.9762	35
TACC3	Transforming acidic coiled-coil containing protein 3	0.9762	35
FGF13	Fibroblast growth factor 13	0.9762	35
H2BC11	H2B clustered histone 11	0.9762	35
PTP4A1	Protein tyrosine phosphatase 4A1	0.9762	35
GDPD3	Glycerophosphodiester phosphodiesterase domain containing 3	0.9762	35

Adipocytes	0.3 nTPM
Breast	0.4 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	0.3 nTPM
Lung	0.3 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

Astrocytes	3.4 nTPM
Brain	3.4 nTPM

B-cells	0.3 nTPM
Lung	1.3 nTPM
Salivary gland	0.9 nTPM
Thymus	0.5 nTPM
Stomach	0.4 nTPM
Lymph node	0.2 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
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Ciliated cells	1.5 nTPM
Bronchus	2.7 nTPM
Endometrium	1.7 nTPM
Lung	1.5 nTPM
Fallopian tube	0.2 nTPM

Club cells	0.6 nTPM
Lung	0.7 nTPM
Bronchus	0.6 nTPM
Prostate	0.5 nTPM

Endothelial cells	0.8 nTPM
Placenta	5.7 nTPM
Liver	2.5 nTPM
Esophagus	0.8 nTPM
Ovary	0.7 nTPM
Salivary gland	0.6 nTPM
Heart muscle	0.5 nTPM
Endometrium	0.5 nTPM
Skeletal muscle	0.5 nTPM
Prostate	0.5 nTPM
Vascular	0.4 nTPM
Testis	0.3 nTPM
Lung	0.2 nTPM
Thymus	0.2 nTPM
Fallopian tube	0.1 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	0.2 nTPM
Colon	0.7 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.5 nTPM
Liver	3.6 nTPM
Heart muscle	3.0 nTPM
Salivary gland	0.3 nTPM
Placenta	0.2 nTPM
Skeletal muscle	0.2 nTPM
Thymus	0.2 nTPM
Vascular	0.2 nTPM
Breast	0.2 nTPM
Pancreas	0.1 nTPM
Adipose tissue	0.1 nTPM
Fallopian tube	0.1 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.3 nTPM
Lung	1.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.1 nTPM
Colon	0.2 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

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

Macrophages	0.3 nTPM
Skeletal muscle	1.1 nTPM
Bone marrow	1.0 nTPM
Spleen	1.0 nTPM
Salivary gland	0.9 nTPM
Vascular	0.8 nTPM
Lung	0.4 nTPM
Thymus	0.4 nTPM
Prostate	0.3 nTPM
Adipose tissue	0.2 nTPM
Fallopian tube	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Tongue	0.0 nTPM
Breast	0.0 nTPM

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

Cholangiocytes	1.9 nTPM
Liver	1.9 nTPM

Early spermatids	13.8 nTPM
Testis	13.8 nTPM

Plasma cells	0.2 nTPM
Salivary gland	0.9 nTPM
Fallopian tube	0.3 nTPM
Spleen	0.2 nTPM
Thymus	0.2 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	0.2 nTPM
Vascular	0.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.1 nTPM
Salivary gland	0.2 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.3 nTPM
Liver	2.1 nTPM
Salivary gland	0.5 nTPM
Skeletal muscle	0.4 nTPM
Tongue	0.3 nTPM
Vascular	0.3 nTPM
Breast	0.2 nTPM
Placenta	0.1 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.1 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
Thymus	0.0 nTPM

T-cells	0.8 nTPM
Vascular	3.6 nTPM
Endometrium	2.5 nTPM
Esophagus	2.4 nTPM
Skeletal muscle	1.5 nTPM
Lung	1.1 nTPM
Prostate	1.0 nTPM
Kidney	0.9 nTPM
Thymus	0.8 nTPM
Tongue	0.8 nTPM
Liver	0.5 nTPM
PBMC	0.4 nTPM
Salivary gland	0.4 nTPM
Breast	0.3 nTPM
Adipose tissue	0.2 nTPM
Lymph node	0.2 nTPM
Bone marrow	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Skin	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Undifferentiated cells	0.3 nTPM
Rectum	0.5 nTPM
Colon	0.3 nTPM
Small intestine	0.1 nTPM

Amygdala excitatory	11.4 nTPM
Hippocampus	13.4 nTPM
Thalamus	13.2 nTPM
Cerebral cortex	12.2 nTPM
Amygdala	11.3 nTPM
Basal ganglia	10.5 nTPM
Hypothalamus	7.9 nTPM

Astrocyte	2.3 nTPM
Basal ganglia	3.3 nTPM
Hypothalamus	3.1 nTPM
Thalamus	2.8 nTPM
Amygdala	2.6 nTPM
Cerebral cortex	2.6 nTPM
Hippocampus	2.5 nTPM
Midbrain	2.4 nTPM
Pons	2.1 nTPM
Cerebellum	1.6 nTPM
Medulla oblongata	1.4 nTPM
Spinal cord	0.5 nTPM

Bergmann glia	4.1 nTPM
Medulla oblongata	8.5 nTPM
Cerebellum	2.2 nTPM
Pons	1.4 nTPM

Central nervous system macrophage	2.4 nTPM
Hypothalamus	8.6 nTPM
Spinal cord	3.2 nTPM
Medulla oblongata	2.4 nTPM
Pons	2.3 nTPM
Basal ganglia	2.0 nTPM
Cerebellum	1.6 nTPM
Cerebral cortex	1.3 nTPM
Thalamus	1.3 nTPM
Hippocampus	1.2 nTPM
Midbrain	1.2 nTPM
Amygdala	1.0 nTPM

Cerebellar inhibitory	14.6 nTPM
Cerebellum	17.2 nTPM
Medulla oblongata	16.4 nTPM
Spinal cord	13.7 nTPM
Midbrain	13.4 nTPM
Pons	12.3 nTPM

Cge interneuron	8.2 nTPM
Midbrain	9.9 nTPM
Cerebral cortex	9.6 nTPM
Amygdala	8.5 nTPM
Thalamus	7.9 nTPM
Basal ganglia	7.6 nTPM
Hippocampus	7.2 nTPM
Hypothalamus	6.5 nTPM

Choroid plexus epithelial cell	0.5 nTPM
Medulla oblongata	1.0 nTPM
Basal ganglia	0.9 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	1.6 nTPM
Thalamus	4.1 nTPM
Cerebellum	3.2 nTPM
Medulla oblongata	2.6 nTPM
Pons	1.8 nTPM
Amygdala	1.7 nTPM
Hypothalamus	1.4 nTPM
Basal ganglia	1.1 nTPM
Hippocampus	0.8 nTPM
Cerebral cortex	0.6 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	12.1 nTPM
Cerebral cortex	12.7 nTPM
Amygdala	12.2 nTPM
Basal ganglia	12.2 nTPM
Midbrain	12.2 nTPM
Hypothalamus	11.7 nTPM
Hippocampus	11.6 nTPM

Deep-layer intratelencephalic	10.0 nTPM
Amygdala	10.5 nTPM
Basal ganglia	10.3 nTPM
Cerebral cortex	10.1 nTPM
Hippocampus	9.7 nTPM
Hypothalamus	9.4 nTPM

Deep-layer near-projecting	12.0 nTPM
Amygdala	13.2 nTPM
Cerebral cortex	12.9 nTPM
Hippocampus	12.7 nTPM
Hypothalamus	11.6 nTPM
Basal ganglia	9.7 nTPM

Eccentric medium spiny neuron	6.5 nTPM
Cerebral cortex	7.6 nTPM
Amygdala	7.3 nTPM
Basal ganglia	7.0 nTPM
Hypothalamus	6.2 nTPM
Thalamus	5.7 nTPM
Hippocampus	5.4 nTPM

Endothelial cell	3.7 nTPM
Basal ganglia	9.3 nTPM
Cerebral cortex	7.7 nTPM
Midbrain	4.7 nTPM
Thalamus	4.0 nTPM
Hippocampus	3.8 nTPM
Medulla oblongata	3.1 nTPM
Hypothalamus	2.5 nTPM
Pons	2.5 nTPM
Cerebellum	1.5 nTPM
Amygdala	1.1 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	1.5 nTPM
Hypothalamus	3.6 nTPM
Thalamus	2.4 nTPM
Midbrain	1.9 nTPM
Pons	1.6 nTPM
Medulla oblongata	1.5 nTPM
Amygdala	1.1 nTPM
Basal ganglia	0.9 nTPM
Hippocampus	0.6 nTPM
Spinal cord	0.0 nTPM