Single cell type - SOCS6 - The Human Protein Atlas

SOCS6

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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.	SOCS6
Gene descriptionⁱ Full gene name according to HGNC.	Suppressor of cytokine signaling 6
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.	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 (Microglial 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.	0.42
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 enriched (Central nervous system macrophage)
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 (myeloid DC, classical monocyte)
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 (Microglial 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: Cell type enriched (Central nervous system macrophage)

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 (myeloid DC, classical monocyte)
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

SOCS6 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.
SIGLEC8	Sialic acid binding Ig like lectin 8	0.4583	30
CPM	Carboxypeptidase M	0.4371	58
P2RX4	Purinergic receptor P2X 4	0.4318	24
TM9SF3	Transmembrane 9 superfamily member 3	0.4233	16
PPARD	Peroxisome proliferator activated receptor delta	0.4190	45
EGR2	Early growth response 2	0.4180	58
FOSB	FosB proto-oncogene, AP-1 transcription factor subunit	0.4145	80
BMP2K	BMP2 inducible kinase	0.4121	30
BACE2	Beta-secretase 2	0.4100	45
RNF223	Ring finger protein 223	0.4084	37
GSE1	Gse1 coiled-coil protein	0.4083	27
CYFIP1	Cytoplasmic FMR1 interacting protein 1	0.4083	58
EGR3	Early growth response 3	0.4044	80
ENSG00000250644	Novel protein	0.4040	58
NUFIP2	Nuclear FMR1 interacting protein 2	0.4033	80

IMMUNE CELLS

SOCS6 is part of cluster 29 Non-specific - Unknown function with confidenceⁱ 0.66
401 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.
ATP5F1E	ATP synthase F1 subunit epsilon	0.9762	29
CD300LB	CD300 molecule like family member b	0.9762	29
ENSG00000288053	Novel protein	0.9524	29
MYCBP	MYC binding protein	0.9524	29
PYCARD	PYD and CARD domain containing	0.9524	7
USP32	Ubiquitin specific peptidase 32	0.9524	29
RILP	Rab interacting lysosomal protein	0.9524	29
HDGF	Heparin binding growth factor	0.9286	29
RALGAPA2	Ral GTPase activating protein catalytic subunit alpha 2	0.9286	29
ZNF223	Zinc finger protein 223	0.9286	29
JAML	Junction adhesion molecule like	0.9286	7
IL18	Interleukin 18	0.9286	29
THBS1	Thrombospondin 1	0.9286	7
PGLS	6-phosphogluconolactonase	0.9286	29
HM13	Histocompatibility minor 13	0.9286	29

Adipocytes	14.1 nTPM
Adipose tissue	16.0 nTPM
Breast	12.2 nTPM

Alveolar cells type 1	25.8 nTPM
Lung	25.8 nTPM

Alveolar cells type 2	10.1 nTPM
Lung	10.1 nTPM

Astrocytes	7.7 nTPM
Brain	7.7 nTPM

B-cells	1.5 nTPM
Skin	11.9 nTPM
Adipose tissue	2.9 nTPM
Salivary gland	1.4 nTPM
Stomach	1.3 nTPM
Lung	1.3 nTPM
Thymus	0.9 nTPM
Lymph node	0.2 nTPM
Spleen	0.2 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Ciliated cells	16.1 nTPM
Endometrium	18.9 nTPM
Bronchus	17.5 nTPM
Lung	15.6 nTPM
Fallopian tube	12.6 nTPM

Club cells	22.0 nTPM
Bronchus	26.6 nTPM
Lung	23.2 nTPM
Prostate	16.1 nTPM

Endothelial cells	13.4 nTPM
Pancreas	23.3 nTPM
Salivary gland	16.8 nTPM
Breast	16.7 nTPM
Skin	16.6 nTPM
Heart muscle	15.4 nTPM
Prostate	14.7 nTPM
Skeletal muscle	14.0 nTPM
Liver	13.9 nTPM
Endometrium	13.9 nTPM
Vascular	13.1 nTPM
Fallopian tube	12.7 nTPM
Tongue	12.6 nTPM
Esophagus	11.2 nTPM
Placenta	10.8 nTPM
Ovary	10.1 nTPM
Testis	9.5 nTPM
Thymus	9.0 nTPM
Lung	7.2 nTPM

Enteroendocrine cells	26.1 nTPM
Colon	29.1 nTPM
Rectum	28.5 nTPM
Small intestine	20.6 nTPM

Fibroblasts	13.4 nTPM
Placenta	24.3 nTPM
Heart muscle	17.3 nTPM
Prostate	16.5 nTPM
Skin	16.3 nTPM
Adipose tissue	16.1 nTPM
Fallopian tube	15.6 nTPM
Liver	14.2 nTPM
Skeletal muscle	13.1 nTPM
Pancreas	13.0 nTPM
Salivary gland	11.7 nTPM
Breast	11.3 nTPM
Esophagus	10.8 nTPM
Vascular	10.3 nTPM
Thymus	9.8 nTPM
Stomach	7.2 nTPM
Lung	6.7 nTPM

Granulocytes	29.4 nTPM
Fallopian tube	44.0 nTPM
Lung	24.7 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	41.8 nTPM
Small intestine	64.3 nTPM
Colon	33.0 nTPM
Rectum	28.1 nTPM

Lymphatic endothelial cells	15.8 nTPM
Fallopian tube	20.7 nTPM
Ovary	10.9 nTPM

Macrophages	20.6 nTPM
Salivary gland	57.2 nTPM
Prostate	43.4 nTPM
Breast	38.5 nTPM
Fallopian tube	30.9 nTPM
Lung	27.8 nTPM
Testis	26.0 nTPM
Vascular	25.0 nTPM
Skin	20.1 nTPM
Esophagus	18.0 nTPM
Kidney	15.9 nTPM
Adipose tissue	13.9 nTPM
Thymus	11.5 nTPM
Skeletal muscle	10.7 nTPM
Tongue	10.3 nTPM
Endometrium	9.2 nTPM
Pancreas	8.2 nTPM
Bone marrow	8.1 nTPM
Spleen	8.0 nTPM
Stomach	7.7 nTPM

Paneth cells	22.9 nTPM
Rectum	26.5 nTPM
Small intestine	24.2 nTPM
Colon	18.1 nTPM

Basal keratinocytes	13.7 nTPM
Tongue	13.7 nTPM
Skin	13.6 nTPM

Basal prostatic cells	11.1 nTPM
Prostate	11.1 nTPM

Basal squamous epithelial cells	12.4 nTPM
Esophagus	12.4 nTPM

Bipolar cells	10.4 nTPM
Eye	10.4 nTPM

Plasma cells	1.9 nTPM
Fallopian tube	6.1 nTPM
Salivary gland	5.4 nTPM
Liver	1.5 nTPM
Thymus	1.2 nTPM
Stomach	0.8 nTPM
Spleen	0.2 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	11.4 nTPM
Adipose tissue	22.6 nTPM
Vascular	11.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	10.8 nTPM
Salivary gland	17.2 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	11.0 nTPM
Tongue	15.0 nTPM
Endometrium	14.2 nTPM
Liver	13.2 nTPM
Skin	12.8 nTPM
Placenta	12.2 nTPM
Skeletal muscle	12.2 nTPM
Prostate	12.2 nTPM
Adipose tissue	12.0 nTPM
Vascular	11.9 nTPM
Salivary gland	11.5 nTPM
Fallopian tube	11.2 nTPM
Breast	9.9 nTPM
Lung	8.2 nTPM
Thymus	7.9 nTPM
Ovary	6.3 nTPM
Esophagus	4.8 nTPM

Suprabasal keratinocytes	24.9 nTPM
Tongue	36.7 nTPM
Skin	13.1 nTPM

T-cells	1.8 nTPM
Vascular	5.2 nTPM
Endometrium	4.3 nTPM
Tongue	3.3 nTPM
Colon	2.9 nTPM
Skin	2.8 nTPM
Prostate	2.7 nTPM
Salivary gland	2.7 nTPM
Kidney	1.8 nTPM
Liver	1.7 nTPM
Breast	1.5 nTPM
Thymus	1.2 nTPM
PBMC	1.1 nTPM
Spleen	1.0 nTPM
Adipose tissue	0.9 nTPM
Stomach	0.9 nTPM
Skeletal muscle	0.8 nTPM
Lymph node	0.7 nTPM
Lung	0.5 nTPM
Fallopian tube	0.5 nTPM
Bone marrow	0.3 nTPM
Esophagus	0.0 nTPM

Undifferentiated cells	22.4 nTPM
Small intestine	24.0 nTPM
Colon	21.7 nTPM
Rectum	21.4 nTPM

Amygdala excitatory	23.4 nTPM
Hypothalamus	30.5 nTPM
Thalamus	25.0 nTPM
Basal ganglia	24.4 nTPM
Amygdala	22.8 nTPM
Hippocampus	19.6 nTPM
Cerebral cortex	18.3 nTPM

Astrocyte	21.8 nTPM
Amygdala	33.4 nTPM
Hippocampus	25.5 nTPM
Cerebral cortex	24.9 nTPM
Basal ganglia	23.8 nTPM
Midbrain	21.8 nTPM
Thalamus	21.0 nTPM
Hypothalamus	19.0 nTPM
Medulla oblongata	18.9 nTPM
Cerebellum	18.8 nTPM
Pons	18.7 nTPM
Spinal cord	13.7 nTPM

Bergmann glia	25.9 nTPM
Cerebellum	33.2 nTPM
Pons	27.3 nTPM
Medulla oblongata	17.0 nTPM

Central nervous system macrophage	633.7 nTPM
Basal ganglia	759.4 nTPM
Midbrain	719.2 nTPM
Cerebellum	690.9 nTPM
Amygdala	678.1 nTPM
Hippocampus	661.7 nTPM
Thalamus	643.2 nTPM
Pons	635.9 nTPM
Hypothalamus	625.1 nTPM
Cerebral cortex	588.4 nTPM
Medulla oblongata	497.1 nTPM
Spinal cord	471.9 nTPM

Cerebellar inhibitory	20.8 nTPM
Spinal cord	24.7 nTPM
Pons	23.5 nTPM
Cerebellum	20.7 nTPM
Medulla oblongata	18.8 nTPM
Midbrain	16.5 nTPM

Cge interneuron	21.9 nTPM
Hypothalamus	25.1 nTPM
Midbrain	22.1 nTPM
Thalamus	21.6 nTPM
Amygdala	21.4 nTPM
Basal ganglia	21.1 nTPM
Cerebral cortex	20.9 nTPM
Hippocampus	20.8 nTPM

Choroid plexus epithelial cell	34.3 nTPM
Basal ganglia	58.0 nTPM
Medulla oblongata	32.2 nTPM
Hippocampus	30.5 nTPM
Thalamus	16.4 nTPM

Committed oligodendrocyte precursor	34.2 nTPM
Thalamus	46.6 nTPM
Basal ganglia	44.3 nTPM
Hypothalamus	40.3 nTPM
Spinal cord	36.8 nTPM
Cerebral cortex	36.7 nTPM
Cerebellum	36.5 nTPM
Medulla oblongata	29.7 nTPM
Amygdala	29.3 nTPM
Hippocampus	29.2 nTPM
Midbrain	23.5 nTPM
Pons	23.0 nTPM

Deep-layer corticothalamic and 6b	29.6 nTPM
Midbrain	37.7 nTPM
Hypothalamus	37.3 nTPM
Basal ganglia	26.4 nTPM
Cerebral cortex	26.2 nTPM
Hippocampus	25.0 nTPM
Amygdala	24.8 nTPM

Deep-layer intratelencephalic	22.3 nTPM
Hypothalamus	25.9 nTPM
Amygdala	22.2 nTPM
Cerebral cortex	21.6 nTPM
Basal ganglia	21.0 nTPM
Hippocampus	21.0 nTPM

Deep-layer near-projecting	28.7 nTPM
Hypothalamus	35.5 nTPM
Amygdala	30.9 nTPM
Basal ganglia	28.8 nTPM
Cerebral cortex	24.2 nTPM
Hippocampus	24.1 nTPM

Eccentric medium spiny neuron	37.7 nTPM
Thalamus	52.4 nTPM
Basal ganglia	45.6 nTPM
Hippocampus	34.8 nTPM
Hypothalamus	33.4 nTPM
Cerebral cortex	30.1 nTPM
Amygdala	29.6 nTPM

Endothelial cell	33.2 nTPM
Spinal cord	46.6 nTPM
Amygdala	40.2 nTPM
Thalamus	36.7 nTPM
Hippocampus	36.2 nTPM
Medulla oblongata	35.9 nTPM
Hypothalamus	34.7 nTPM
Pons	31.8 nTPM
Midbrain	29.3 nTPM
Cerebellum	28.7 nTPM
Cerebral cortex	23.7 nTPM
Basal ganglia	21.4 nTPM