Single cell type - SUSD6 - The Human Protein Atlas

SUSD6

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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.	SUSD6
Gene descriptionⁱ Full gene name according to HGNC.	Sushi domain containing 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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 (Microglial cells, Monocytes)
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.	0.35
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 enhanced (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.	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 (Microglial cells, Monocytes)

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 enhanced (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: 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

SUSD6 is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.95
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.
PFKFB3	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	0.5595	29
KDM6B	Lysine demethylase 6B	0.5318	29
CXCL2	C-X-C motif chemokine ligand 2	0.5310	29
CHSY1	Chondroitin sulfate synthase 1	0.5243	29
ICAM1	Intercellular adhesion molecule 1	0.5102	41
MIDN	Midnolin	0.5077	80
DENND3	DENN domain containing 3	0.5038	41
RLIM	Ring finger protein, LIM domain interacting	0.5019	29
TMC4	Transmembrane channel like 4	0.4906	35
CXCL8	C-X-C motif chemokine ligand 8	0.4787	29
CHD1	Chromodomain helicase DNA binding protein 1	0.4779	29
GPR132	G protein-coupled receptor 132	0.4759	29
PLSCR1	Phospholipid scramblase 1	0.4750	29
NINJ1	Ninjurin 1	0.4723	29
IFNGR1	Interferon gamma receptor 1	0.4717	35

IMMUNE CELLS

SUSD6 is part of cluster 37 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 0.93
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.
FRMD3	FERM domain containing 3	1.0000	37
RNF169	Ring finger protein 169	1.0000	37
CAMTA2	Calmodulin binding transcription activator 2	1.0000	37
GLYR1	Glyoxylate reductase 1 homolog	0.9762	40
MCTP1	Multiple C2 and transmembrane domain containing 1	0.9762	37
TLR1	Toll like receptor 1	0.9762	37
JUNB	JunB proto-oncogene, AP-1 transcription factor subunit	0.9762	37
HEY1	Hes related family bHLH transcription factor with YRPW motif 1	0.9762	37
TPCN2	Two pore segment channel 2	0.9762	37
CDC42EP2	CDC42 effector protein 2	0.9762	37
NFKBIZ	NFKB inhibitor zeta	0.9762	37
PLOD1	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1	0.9762	38
DGLUCY	D-glutamate cyclase	0.9762	37
AKAP10	A-kinase anchoring protein 10	0.9762	38
MON1B	MON1 homolog B, secretory trafficking associated	0.9762	38

Adipocytes	43.8 nTPM
Adipose tissue	69.4 nTPM
Breast	18.1 nTPM

Alveolar cells type 1	37.0 nTPM
Lung	37.0 nTPM

Alveolar cells type 2	34.8 nTPM
Lung	34.8 nTPM

Astrocytes	21.1 nTPM
Brain	21.1 nTPM

B-cells	26.7 nTPM
Skin	49.1 nTPM
Lymph node	41.2 nTPM
Stomach	36.7 nTPM
Kidney	31.2 nTPM
Salivary gland	28.1 nTPM
Thymus	27.5 nTPM
Spleen	25.7 nTPM
Adipose tissue	25.1 nTPM
Bone marrow	24.3 nTPM
Lung	21.5 nTPM
PBMC	20.0 nTPM
Esophagus	11.8 nTPM
Liver	4.8 nTPM

Ciliated cells	36.6 nTPM
Bronchus	54.4 nTPM
Fallopian tube	34.2 nTPM
Endometrium	32.2 nTPM
Lung	25.6 nTPM

Club cells	31.6 nTPM
Bronchus	44.9 nTPM
Lung	32.9 nTPM
Prostate	17.0 nTPM

Dendritic cells	45.3 nTPM
Adipose tissue	76.3 nTPM
PBMC	14.4 nTPM

Endothelial cells	30.8 nTPM
Skin	69.6 nTPM
Fallopian tube	57.7 nTPM
Lung	45.3 nTPM
Skeletal muscle	44.8 nTPM
Heart muscle	40.5 nTPM
Salivary gland	40.4 nTPM
Thymus	33.7 nTPM
Endometrium	33.6 nTPM
Pancreas	28.4 nTPM
Vascular	27.9 nTPM
Esophagus	26.3 nTPM
Tongue	24.2 nTPM
Prostate	21.4 nTPM
Placenta	14.8 nTPM
Ovary	14.7 nTPM
Testis	14.0 nTPM
Breast	8.8 nTPM
Liver	7.6 nTPM

Enteroendocrine cells	9.7 nTPM
Small intestine	10.3 nTPM
Rectum	10.1 nTPM
Colon	8.6 nTPM

Fibroblasts	13.3 nTPM
Skeletal muscle	24.8 nTPM
Fallopian tube	23.2 nTPM
Skin	21.4 nTPM
Liver	17.8 nTPM
Pancreas	17.2 nTPM
Lung	14.9 nTPM
Vascular	14.0 nTPM
Thymus	13.7 nTPM
Salivary gland	13.3 nTPM
Adipose tissue	11.8 nTPM
Stomach	10.1 nTPM
Breast	10.1 nTPM
Esophagus	8.0 nTPM
Prostate	5.9 nTPM
Placenta	4.3 nTPM
Heart muscle	2.3 nTPM

Granulocytes	30.4 nTPM
Tongue	34.0 nTPM
Lung	31.8 nTPM
Fallopian tube	25.4 nTPM

Intestinal goblet cells	41.2 nTPM
Small intestine	88.5 nTPM
Rectum	25.7 nTPM
Colon	9.6 nTPM

Lymphatic endothelial cells	11.5 nTPM
Fallopian tube	23.1 nTPM
Ovary	0.0 nTPM

Macrophages	51.4 nTPM
Fallopian tube	109.6 nTPM
Adipose tissue	109.3 nTPM
Spleen	72.2 nTPM
Salivary gland	65.0 nTPM
Skeletal muscle	63.8 nTPM
Tongue	63.4 nTPM
Prostate	61.2 nTPM
Stomach	54.0 nTPM
Skin	44.6 nTPM
Lung	42.0 nTPM
Thymus	41.8 nTPM
Vascular	41.0 nTPM
Esophagus	37.2 nTPM
Breast	36.0 nTPM
Endometrium	35.1 nTPM
Bone marrow	27.4 nTPM
Testis	26.7 nTPM
Kidney	23.0 nTPM
Pancreas	22.6 nTPM

Basal prostatic cells	16.2 nTPM
Prostate	16.2 nTPM

Basal respiratory cells	46.0 nTPM
Bronchus	46.0 nTPM

Basal squamous epithelial cells	25.3 nTPM
Esophagus	25.3 nTPM

Bipolar cells	18.6 nTPM
Eye	18.6 nTPM

Paneth cells	24.6 nTPM
Small intestine	31.1 nTPM
Rectum	24.8 nTPM
Colon	18.1 nTPM

Plasma cells	12.7 nTPM
Salivary gland	26.9 nTPM
Stomach	18.0 nTPM
Fallopian tube	14.8 nTPM
Thymus	10.9 nTPM
Liver	9.0 nTPM
Spleen	8.9 nTPM
Bone marrow	7.6 nTPM
Esophagus	5.2 nTPM

Schwann cells	42.9 nTPM
Adipose tissue	120.2 nTPM
Vascular	8.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	15.2 nTPM
Salivary gland	25.9 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	22.1 nTPM
Skin	59.9 nTPM
Skeletal muscle	41.7 nTPM
Fallopian tube	33.6 nTPM
Adipose tissue	28.3 nTPM
Salivary gland	25.0 nTPM
Thymus	20.8 nTPM
Esophagus	20.4 nTPM
Vascular	17.0 nTPM
Tongue	16.2 nTPM
Endometrium	15.8 nTPM
Liver	15.3 nTPM
Lung	14.1 nTPM
Breast	12.9 nTPM
Prostate	12.8 nTPM
Ovary	11.3 nTPM
Placenta	9.0 nTPM

Suprabasal keratinocytes	28.1 nTPM
Skin	44.0 nTPM
Tongue	12.3 nTPM

T-cells	26.8 nTPM
Adipose tissue	49.5 nTPM
Fallopian tube	42.5 nTPM
Skin	40.7 nTPM
Skeletal muscle	34.4 nTPM
Tongue	32.2 nTPM
Endometrium	30.5 nTPM
Stomach	30.1 nTPM
Lymph node	27.4 nTPM
Colon	27.3 nTPM
Spleen	25.7 nTPM
Lung	25.7 nTPM
Vascular	25.7 nTPM
Thymus	22.6 nTPM
Prostate	21.7 nTPM
Breast	21.7 nTPM
Bone marrow	21.5 nTPM
Salivary gland	21.0 nTPM
Liver	17.1 nTPM
Esophagus	17.0 nTPM
PBMC	14.8 nTPM
Kidney	13.3 nTPM

Undifferentiated cells	9.0 nTPM
Small intestine	14.8 nTPM
Rectum	7.9 nTPM
Colon	4.3 nTPM

Amygdala excitatory	49.9 nTPM
Hypothalamus	62.7 nTPM
Thalamus	54.0 nTPM
Amygdala	52.1 nTPM
Hippocampus	44.6 nTPM
Basal ganglia	43.7 nTPM
Cerebral cortex	42.2 nTPM

Astrocyte	34.7 nTPM
Medulla oblongata	44.6 nTPM
Spinal cord	44.4 nTPM
Pons	35.7 nTPM
Cerebellum	35.1 nTPM
Midbrain	34.4 nTPM
Amygdala	33.6 nTPM
Hippocampus	33.4 nTPM
Hypothalamus	32.2 nTPM
Cerebral cortex	30.6 nTPM
Basal ganglia	28.7 nTPM
Thalamus	28.7 nTPM

Bergmann glia	49.8 nTPM
Cerebellum	59.3 nTPM
Medulla oblongata	55.4 nTPM
Pons	34.5 nTPM

Central nervous system macrophage	549.1 nTPM
Amygdala	715.7 nTPM
Hypothalamus	616.9 nTPM
Hippocampus	557.8 nTPM
Midbrain	557.5 nTPM
Thalamus	550.3 nTPM
Cerebral cortex	534.6 nTPM
Cerebellum	529.6 nTPM
Pons	524.8 nTPM
Basal ganglia	510.9 nTPM
Medulla oblongata	496.8 nTPM
Spinal cord	444.8 nTPM

Cerebellar inhibitory	61.4 nTPM
Medulla oblongata	73.8 nTPM
Cerebellum	70.2 nTPM
Midbrain	60.3 nTPM
Spinal cord	52.2 nTPM
Pons	50.6 nTPM

Cge interneuron	22.8 nTPM
Hypothalamus	30.6 nTPM
Amygdala	23.7 nTPM
Cerebral cortex	23.3 nTPM
Basal ganglia	21.3 nTPM
Thalamus	20.8 nTPM
Hippocampus	20.7 nTPM
Midbrain	19.4 nTPM

Choroid plexus epithelial cell	95.5 nTPM
Basal ganglia	144.5 nTPM
Medulla oblongata	91.4 nTPM
Hippocampus	77.7 nTPM
Thalamus	68.5 nTPM

Committed oligodendrocyte precursor	75.5 nTPM
Spinal cord	117.7 nTPM
Cerebral cortex	97.5 nTPM
Hippocampus	91.3 nTPM
Midbrain	89.0 nTPM
Amygdala	78.9 nTPM
Cerebellum	77.7 nTPM
Basal ganglia	66.3 nTPM
Medulla oblongata	58.1 nTPM
Pons	56.7 nTPM
Hypothalamus	53.9 nTPM
Thalamus	42.8 nTPM

Deep-layer corticothalamic and 6b	71.8 nTPM
Hypothalamus	81.4 nTPM
Cerebral cortex	77.7 nTPM
Amygdala	77.3 nTPM
Basal ganglia	74.2 nTPM
Midbrain	66.6 nTPM
Hippocampus	53.6 nTPM

Deep-layer intratelencephalic	56.3 nTPM
Hypothalamus	75.6 nTPM
Amygdala	54.4 nTPM
Cerebral cortex	52.0 nTPM
Hippocampus	51.8 nTPM
Basal ganglia	47.5 nTPM

Deep-layer near-projecting	36.6 nTPM
Hypothalamus	50.3 nTPM
Amygdala	35.9 nTPM
Basal ganglia	35.4 nTPM
Cerebral cortex	31.3 nTPM
Hippocampus	30.2 nTPM

Eccentric medium spiny neuron	34.0 nTPM
Amygdala	41.0 nTPM
Cerebral cortex	38.2 nTPM
Hippocampus	37.3 nTPM
Thalamus	30.4 nTPM
Hypothalamus	29.9 nTPM
Basal ganglia	26.9 nTPM