Single cell type - GPATCH11 - The Human Protein Atlas

GPATCH11

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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.	GPATCH11
Gene descriptionⁱ Full gene name according to HGNC.	G-patch domain containing 11
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.	2

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 (Spermatocytes)
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 (Spermatocytes)

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

GPATCH11 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.
RPF1	Ribosome production factor 1 homolog	0.5071	15
AGRP	Agouti related neuropeptide	0.4796	58
CHIT1	Chitinase 1	0.4773	58
MARCO	Macrophage receptor with collagenous structure	0.4763	58
VSIG4	V-set and immunoglobulin domain containing 4	0.4726	58
OR6N1	Olfactory receptor family 6 subfamily N member 1	0.4704	58
ZBTB24	Zinc finger and BTB domain containing 24	0.4677	66
SLU7	SLU7 homolog, splicing factor	0.4623	55
USF2	Upstream transcription factor 2, c-fos interacting	0.4603	58
GM2A	Ganglioside GM2 activator	0.4589	58
ABCG1	ATP binding cassette subfamily G member 1	0.4566	58
DCSTAMP	Dendrocyte expressed seven transmembrane protein	0.4543	58
MSR1	Macrophage scavenger receptor 1	0.4520	58
TRPV2	Transient receptor potential cation channel subfamily V member 2	0.4508	58
ACP5	Acid phosphatase 5, tartrate resistant	0.4473	58

IMMUNE CELLS

GPATCH11 is part of cluster 41 Basophils - Unknown function with confidenceⁱ 0.91
293 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.
OR2C3	Olfactory receptor family 2 subfamily C member 3	1.0000	41
ZDHHC8	Zinc finger DHHC-type palmitoyltransferase 8	1.0000	41
CTCF	CCCTC-binding factor	1.0000	41
ZNF618	Zinc finger protein 618	1.0000	41
AHI1	Abelson helper integration site 1	0.9762	41
DNAJB13	DnaJ heat shock protein family (Hsp40) member B13	0.9762	41
IL3RA	Interleukin 3 receptor subunit alpha	0.9762	41
ZNF329	Zinc finger protein 329	0.9762	41
SWI5	SWI5 homologous recombination repair protein	0.9762	41
NEMF	Nuclear export mediator factor	0.9762	41
NEK8	NIMA related kinase 8	0.9762	41
FAM149B1	Family with sequence similarity 149 member B1	0.9762	41
MPND	MPN domain containing	0.9762	10
AP4B1	Adaptor related protein complex 4 subunit beta 1	0.9762	41
CHD1L	Chromodomain helicase DNA binding protein 1 like	0.9762	41

Adipocytes	13.8 nTPM
Breast	14.8 nTPM
Adipose tissue	12.9 nTPM

Alveolar cells type 1	13.1 nTPM
Lung	13.1 nTPM

Alveolar cells type 2	10.9 nTPM
Lung	10.9 nTPM

Astrocytes	3.7 nTPM
Brain	3.7 nTPM

B-cells	26.1 nTPM
PBMC	55.4 nTPM
Lung	44.3 nTPM
Salivary gland	40.9 nTPM
Thymus	39.0 nTPM
Liver	38.6 nTPM
Adipose tissue	28.8 nTPM
Lymph node	20.7 nTPM
Esophagus	17.7 nTPM
Spleen	17.2 nTPM
Bone marrow	12.1 nTPM
Stomach	11.4 nTPM
Kidney	10.4 nTPM
Skin	3.4 nTPM

Ciliated cells	10.0 nTPM
Endometrium	13.7 nTPM
Lung	11.4 nTPM
Fallopian tube	9.7 nTPM
Bronchus	5.5 nTPM

Club cells	8.1 nTPM
Lung	10.6 nTPM
Prostate	9.5 nTPM
Bronchus	4.1 nTPM

Dendritic cells	55.6 nTPM
PBMC	82.7 nTPM
Adipose tissue	28.4 nTPM

Endothelial cells	15.3 nTPM
Salivary gland	27.7 nTPM
Vascular	26.0 nTPM
Heart muscle	24.9 nTPM
Lung	21.8 nTPM
Fallopian tube	18.3 nTPM
Tongue	17.8 nTPM
Thymus	17.4 nTPM
Prostate	17.1 nTPM
Endometrium	16.6 nTPM
Testis	13.1 nTPM
Ovary	12.6 nTPM
Skeletal muscle	12.5 nTPM
Esophagus	10.8 nTPM
Breast	10.5 nTPM
Skin	9.3 nTPM
Placenta	7.9 nTPM
Liver	7.6 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	6.8 nTPM
Small intestine	13.7 nTPM
Colon	5.1 nTPM
Rectum	1.7 nTPM

Fibroblasts	14.7 nTPM
Salivary gland	23.0 nTPM
Heart muscle	21.8 nTPM
Vascular	20.6 nTPM
Pancreas	19.5 nTPM
Liver	17.8 nTPM
Adipose tissue	17.2 nTPM
Breast	15.9 nTPM
Thymus	15.6 nTPM
Lung	15.2 nTPM
Skeletal muscle	12.9 nTPM
Prostate	12.5 nTPM
Fallopian tube	10.6 nTPM
Stomach	10.1 nTPM
Esophagus	9.9 nTPM
Skin	9.1 nTPM
Placenta	4.3 nTPM

Granulocytes	20.9 nTPM
Fallopian tube	23.1 nTPM
Lung	20.2 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	7.4 nTPM
Small intestine	11.9 nTPM
Colon	6.4 nTPM
Rectum	3.9 nTPM

Lymphatic endothelial cells	18.1 nTPM
Fallopian tube	19.8 nTPM
Ovary	16.4 nTPM

Macrophages	24.1 nTPM
Lung	63.0 nTPM
Adipose tissue	38.8 nTPM
Prostate	34.3 nTPM
Vascular	30.7 nTPM
Salivary gland	30.2 nTPM
Testis	28.5 nTPM
Thymus	27.6 nTPM
Endometrium	26.4 nTPM
Pancreas	22.6 nTPM
Breast	22.5 nTPM
Tongue	20.3 nTPM
Skin	20.1 nTPM
Fallopian tube	17.4 nTPM
Skeletal muscle	16.3 nTPM
Stomach	12.9 nTPM
Esophagus	12.8 nTPM
Kidney	12.4 nTPM
Bone marrow	12.2 nTPM
Spleen	9.0 nTPM

Basal prostatic cells	13.5 nTPM
Prostate	13.5 nTPM

Basal respiratory cells	5.8 nTPM
Bronchus	5.8 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Collecting duct cells	7.8 nTPM
Kidney	7.8 nTPM

Paneth cells	5.8 nTPM
Colon	7.2 nTPM
Small intestine	6.9 nTPM
Rectum	3.2 nTPM

Plasma cells	22.2 nTPM
Esophagus	46.8 nTPM
Liver	25.0 nTPM
Thymus	24.4 nTPM
Salivary gland	19.7 nTPM
Bone marrow	18.1 nTPM
Spleen	17.1 nTPM
Stomach	14.7 nTPM
Fallopian tube	11.9 nTPM

Schwann cells	17.0 nTPM
Vascular	28.7 nTPM
Esophagus	12.0 nTPM
Adipose tissue	10.1 nTPM

Serous glandular cells	8.7 nTPM
Salivary gland	13.0 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	13.5 nTPM
Liver	22.9 nTPM
Vascular	20.5 nTPM
Endometrium	19.5 nTPM
Tongue	17.1 nTPM
Salivary gland	15.7 nTPM
Lung	15.3 nTPM
Ovary	14.7 nTPM
Adipose tissue	14.3 nTPM
Prostate	13.4 nTPM
Thymus	12.8 nTPM
Breast	12.1 nTPM
Placenta	10.1 nTPM
Fallopian tube	9.4 nTPM
Skeletal muscle	8.9 nTPM
Skin	7.6 nTPM
Esophagus	2.4 nTPM

Suprabasal keratinocytes	14.1 nTPM
Tongue	20.9 nTPM
Skin	7.3 nTPM

T-cells	19.0 nTPM
Prostate	39.4 nTPM
Fallopian tube	30.3 nTPM
Adipose tissue	25.2 nTPM
PBMC	24.3 nTPM
Salivary gland	23.8 nTPM
Vascular	22.5 nTPM
Tongue	22.0 nTPM
Endometrium	21.3 nTPM
Lung	21.3 nTPM
Thymus	19.8 nTPM
Liver	19.3 nTPM
Skeletal muscle	17.8 nTPM
Kidney	16.0 nTPM
Breast	15.9 nTPM
Spleen	13.2 nTPM
Colon	12.7 nTPM
Lymph node	12.3 nTPM
Stomach	12.3 nTPM
Bone marrow	12.2 nTPM
Skin	10.5 nTPM
Esophagus	7.3 nTPM

Undifferentiated cells	6.1 nTPM
Colon	8.1 nTPM
Rectum	5.9 nTPM
Small intestine	4.3 nTPM

Amygdala excitatory	17.2 nTPM
Basal ganglia	19.0 nTPM
Hippocampus	18.8 nTPM
Cerebral cortex	18.0 nTPM
Amygdala	17.2 nTPM
Hypothalamus	15.7 nTPM
Thalamus	14.5 nTPM

Astrocyte	11.7 nTPM
Amygdala	13.1 nTPM
Cerebral cortex	13.1 nTPM
Thalamus	12.9 nTPM
Midbrain	12.8 nTPM
Basal ganglia	12.6 nTPM
Hippocampus	12.3 nTPM
Cerebellum	11.9 nTPM
Pons	10.9 nTPM
Medulla oblongata	10.8 nTPM
Hypothalamus	10.7 nTPM
Spinal cord	7.3 nTPM

Bergmann glia	16.0 nTPM
Cerebellum	18.0 nTPM
Pons	17.3 nTPM
Medulla oblongata	12.8 nTPM

Central nervous system macrophage	47.5 nTPM
Basal ganglia	51.0 nTPM
Spinal cord	50.9 nTPM
Amygdala	50.5 nTPM
Midbrain	50.3 nTPM
Hypothalamus	48.1 nTPM
Thalamus	47.8 nTPM
Cerebral cortex	46.3 nTPM
Hippocampus	46.2 nTPM
Medulla oblongata	44.5 nTPM
Pons	43.9 nTPM
Cerebellum	42.5 nTPM

Cerebellar inhibitory	19.5 nTPM
Medulla oblongata	21.0 nTPM
Cerebellum	19.9 nTPM
Pons	19.9 nTPM
Spinal cord	19.2 nTPM
Midbrain	17.4 nTPM

Cge interneuron	23.2 nTPM
Thalamus	30.5 nTPM
Hippocampus	25.8 nTPM
Midbrain	23.6 nTPM
Cerebral cortex	23.1 nTPM
Basal ganglia	22.6 nTPM
Amygdala	20.3 nTPM
Hypothalamus	16.2 nTPM

Choroid plexus epithelial cell	12.1 nTPM
Thalamus	13.7 nTPM
Medulla oblongata	12.1 nTPM
Basal ganglia	11.4 nTPM
Hippocampus	11.1 nTPM

Committed oligodendrocyte precursor	14.4 nTPM
Thalamus	17.6 nTPM
Hippocampus	16.8 nTPM
Cerebellum	15.9 nTPM
Hypothalamus	15.7 nTPM
Medulla oblongata	15.5 nTPM
Amygdala	15.2 nTPM
Pons	15.1 nTPM
Midbrain	13.4 nTPM
Basal ganglia	12.6 nTPM
Spinal cord	11.0 nTPM
Cerebral cortex	9.5 nTPM

Deep-layer corticothalamic and 6b	18.0 nTPM
Basal ganglia	20.8 nTPM
Cerebral cortex	19.9 nTPM
Hippocampus	19.8 nTPM
Amygdala	18.5 nTPM
Hypothalamus	15.7 nTPM
Midbrain	13.3 nTPM

Deep-layer intratelencephalic	19.1 nTPM
Hippocampus	22.3 nTPM
Cerebral cortex	22.0 nTPM
Basal ganglia	19.4 nTPM
Amygdala	17.7 nTPM
Hypothalamus	13.9 nTPM

Deep-layer near-projecting	22.7 nTPM
Hippocampus	30.2 nTPM
Cerebral cortex	23.1 nTPM
Basal ganglia	22.7 nTPM
Hypothalamus	19.5 nTPM
Amygdala	18.0 nTPM

Eccentric medium spiny neuron	22.8 nTPM
Hypothalamus	27.5 nTPM
Thalamus	23.3 nTPM
Basal ganglia	23.1 nTPM
Amygdala	22.0 nTPM
Hippocampus	21.1 nTPM
Cerebral cortex	20.0 nTPM