Single cell type - SDS - The Human Protein Atlas

SDS

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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.	SDS
Gene descriptionⁱ Full gene name according to HGNC.	Serine dehydratase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic proteins 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.	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.	Hepatocytes - Metabolism (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 (Hepatocytes, Hofbauer cells, Langerhans cells, Macrophages, Kupffer 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.	0.89
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.	Group enriched (Astrocyte, Bergmann glia)
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 enriched (myeloid DC)
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 (Hepatocytes, Hofbauer cells, Langerhans cells, Macrophages, Kupffer 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: Group enriched (Astrocyte, Bergmann glia)

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 enriched (myeloid DC)
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

SDS is part of cluster 43 Hepatocytes - Metabolism with confidenceⁱ 1
200 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.
HAMP	Hepcidin antimicrobial peptide	0.7022	43
CYP2E1	Cytochrome P450 family 2 subfamily E member 1	0.6757	43
PON1	Paraoxonase 1	0.6727	43
MASP2	MBL associated serine protease 2	0.6696	43
AMBP	Alpha-1-microglobulin/bikunin precursor	0.6684	43
CFHR2	Complement factor H related 2	0.6669	43
ORM2	Orosomucoid 2	0.6657	43
ATF5	Activating transcription factor 5	0.6639	62
APOC1	Apolipoprotein C1	0.6638	43
APCS	Amyloid P component, serum	0.6637	43
CPB2	Carboxypeptidase B2	0.6625	43
APOA2	Apolipoprotein A2	0.6623	43
HP	Haptoglobin	0.6600	43
PLGLB2	Plasminogen like B2	0.6595	43
SLCO1B1	Solute carrier organic anion transporter family member 1B1	0.6592	43

IMMUNE CELLS

SDS is part of cluster 2 Dendritic cells - Unknown function with confidenceⁱ 0.85
342 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.
C1orf54	Chromosome 1 open reading frame 54	0.9762	2
GM2A	Ganglioside GM2 activator	0.9762	2
CD1C	CD1c molecule	0.9762	2
SLAMF9	SLAM family member 9	0.9762	2
CD1E	CD1e molecule	0.9524	2
ENSG00000259171	Novel protein, ANG-RNASE4 readthrough	0.9524	2
GPR33	G protein-coupled receptor 33	0.9524	2
ZNF366	Zinc finger protein 366	0.9524	2
XCR1	X-C motif chemokine receptor 1	0.9524	2
ALCAM	Activated leukocyte cell adhesion molecule	0.9524	2
TVP23A	Trans-golgi network vesicle protein 23 homolog A	0.9524	2
GEM	GTP binding protein overexpressed in skeletal muscle	0.9524	2
APOC1	Apolipoprotein C1	0.9524	2
OLFML3	Olfactomedin like 3	0.9524	2
TFEC	Transcription factor EC	0.9286	2

Adipocytes	0.2 nTPM
Breast	0.5 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.2 nTPM
Lung	0.2 nTPM

Alveolar cells type 2	0.1 nTPM
Lung	0.1 nTPM

Astrocytes	14.2 nTPM
Brain	14.2 nTPM

B-cells	4.1 nTPM
Liver	48.3 nTPM
Skin	5.1 nTPM
Lymph node	0.1 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	0.4 nTPM
Fallopian tube	1.6 nTPM
Lung	0.2 nTPM
Endometrium	0.1 nTPM
Bronchus	0.0 nTPM

Club cells	0.2 nTPM
Prostate	0.5 nTPM
Lung	0.1 nTPM
Bronchus	0.0 nTPM

Endothelial cells	2.6 nTPM
Liver	39.0 nTPM
Placenta	3.4 nTPM
Skin	1.1 nTPM
Tongue	0.8 nTPM
Lung	0.5 nTPM
Skeletal muscle	0.4 nTPM
Vascular	0.4 nTPM
Endometrium	0.2 nTPM
Heart muscle	0.1 nTPM
Thymus	0.1 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	1.5 nTPM
Liver	16.6 nTPM
Placenta	2.1 nTPM
Skin	1.5 nTPM
Fallopian tube	1.4 nTPM
Lung	1.2 nTPM
Pancreas	0.4 nTPM
Thymus	0.3 nTPM
Vascular	0.3 nTPM
Breast	0.3 nTPM
Salivary gland	0.2 nTPM
Skeletal muscle	0.1 nTPM
Adipose tissue	0.1 nTPM
Esophagus	0.1 nTPM
Heart muscle	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.0 nTPM

Macrophages	79.2 nTPM
Skin	441.3 nTPM
Pancreas	281.6 nTPM
Fallopian tube	159.7 nTPM
Adipose tissue	110.1 nTPM
Esophagus	97.6 nTPM
Kidney	70.8 nTPM
Breast	61.6 nTPM
Endometrium	58.4 nTPM
Tongue	38.1 nTPM
Prostate	37.6 nTPM
Skeletal muscle	37.3 nTPM
Stomach	23.1 nTPM
Thymus	19.2 nTPM
Salivary gland	17.3 nTPM
Vascular	16.3 nTPM
Lung	14.4 nTPM
Spleen	11.0 nTPM
Bone marrow	10.1 nTPM
Testis	0.0 nTPM

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

Cholangiocytes	11.4 nTPM
Liver	11.4 nTPM

Plasma cells	2.7 nTPM
Liver	20.5 nTPM
Salivary gland	0.4 nTPM
Fallopian tube	0.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM

Schwann cells	0.9 nTPM
Adipose tissue	2.7 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.1 nTPM
Salivary gland	0.3 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	1.2 nTPM
Liver	13.6 nTPM
Skin	2.5 nTPM
Lung	1.2 nTPM
Adipose tissue	0.4 nTPM
Placenta	0.3 nTPM
Skeletal muscle	0.3 nTPM
Thymus	0.3 nTPM
Tongue	0.3 nTPM
Breast	0.3 nTPM
Endometrium	0.2 nTPM
Vascular	0.2 nTPM
Fallopian tube	0.2 nTPM
Ovary	0.1 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM

T-cells	2.1 nTPM
Liver	28.8 nTPM
Colon	7.8 nTPM
Skin	4.2 nTPM
Lung	1.6 nTPM
Endometrium	0.4 nTPM
Skeletal muscle	0.4 nTPM
Salivary gland	0.4 nTPM
Adipose tissue	0.3 nTPM
Breast	0.3 nTPM
PBMC	0.2 nTPM
Fallopian tube	0.2 nTPM
Thymus	0.1 nTPM
Kidney	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	0.3 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.5 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.3 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.0 nTPM

Astrocyte	42.6 nTPM
Basal ganglia	76.7 nTPM
Midbrain	70.8 nTPM
Cerebellum	55.8 nTPM
Thalamus	51.0 nTPM
Hippocampus	45.6 nTPM
Pons	43.4 nTPM
Cerebral cortex	33.3 nTPM
Amygdala	28.3 nTPM
Medulla oblongata	25.9 nTPM
Hypothalamus	21.6 nTPM
Spinal cord	16.3 nTPM

Bergmann glia	28.5 nTPM
Pons	34.5 nTPM
Cerebellum	27.6 nTPM
Medulla oblongata	23.4 nTPM

Central nervous system macrophage	1.6 nTPM
Spinal cord	3.2 nTPM
Amygdala	3.0 nTPM
Hypothalamus	2.1 nTPM
Medulla oblongata	1.5 nTPM
Basal ganglia	1.4 nTPM
Pons	1.4 nTPM
Cerebellum	1.1 nTPM
Midbrain	1.1 nTPM
Hippocampus	1.0 nTPM
Thalamus	0.9 nTPM
Cerebral cortex	0.5 nTPM

Cerebellar inhibitory	1.8 nTPM
Spinal cord	5.5 nTPM
Medulla oblongata	1.5 nTPM
Cerebellum	1.0 nTPM
Pons	0.9 nTPM
Midbrain	0.0 nTPM

Cge interneuron	0.5 nTPM
Midbrain	0.7 nTPM
Cerebral cortex	0.5 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.4 nTPM
Hippocampus	0.4 nTPM
Hypothalamus	0.4 nTPM
Thalamus	0.3 nTPM

Choroid plexus epithelial cell	0.3 nTPM
Medulla oblongata	1.0 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	0.5 nTPM
Basal ganglia	1.6 nTPM
Hypothalamus	1.4 nTPM
Pons	0.9 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.5 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.7 nTPM
Midbrain	1.1 nTPM
Hippocampus	0.8 nTPM
Amygdala	0.7 nTPM
Cerebral cortex	0.7 nTPM
Basal ganglia	0.6 nTPM
Hypothalamus	0.3 nTPM

Deep-layer intratelencephalic	0.5 nTPM
Hippocampus	0.7 nTPM
Amygdala	0.6 nTPM
Basal ganglia	0.6 nTPM
Cerebral cortex	0.6 nTPM
Hypothalamus	0.2 nTPM

Deep-layer near-projecting	0.7 nTPM
Hippocampus	1.6 nTPM
Amygdala	0.7 nTPM
Basal ganglia	0.7 nTPM
Cerebral cortex	0.5 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.3 nTPM
Basal ganglia	0.5 nTPM
Cerebral cortex	0.5 nTPM
Thalamus	0.5 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.2 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	0.3 nTPM
Medulla oblongata	2.1 nTPM
Hippocampus	0.6 nTPM
Thalamus	0.6 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

Ependymal cell	0.8 nTPM
Amygdala	2.3 nTPM
Thalamus	1.2 nTPM
Hypothalamus	0.9 nTPM
Hippocampus	0.7 nTPM
Basal ganglia	0.6 nTPM
Midbrain	0.6 nTPM
Medulla oblongata	0.4 nTPM
Pons	0.4 nTPM
Spinal cord	0.0 nTPM