Single cell type - SMOC1 - The Human Protein Atlas

SMOC1

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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.	SMOC1
Gene descriptionⁱ Full gene name according to HGNC.	SPARC related modular calcium binding 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Human disease related genes
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.	Secreted
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.	Oligodendrocyte precursor - Unknown function (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 (Oligodendrocyte precursor cells, Peritubular cells, Hepatocytes, Oligodendrocytes)
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.	0.80
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 (Committed oligodendrocyte precursor, Oligodendrocyte precursor cell, Ependymal cell)
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 (plasmacytoid 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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 (Oligodendrocyte precursor cells, Peritubular cells, Hepatocytes, Oligodendrocytes)

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 (Committed oligodendrocyte precursor, Oligodendrocyte precursor cell, Ependymal cell)

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 (plasmacytoid 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

SMOC1 is part of cluster 76 Oligodendrocyte precursor - Unknown function with confidenceⁱ 1
210 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.
PLPPR1	Phospholipid phosphatase related 1	0.8308	76
OLIG2	Oligodendrocyte transcription factor 2	0.8283	76
OLIG1	Oligodendrocyte transcription factor 1	0.8026	76
GPR17	G protein-coupled receptor 17	0.7978	76
PCDH15	Protocadherin related 15	0.7937	76
LHFPL3	LHFPL tetraspan subfamily member 3	0.7879	76
PTPRZ1	Protein tyrosine phosphatase receptor type Z1	0.7754	76
STK32A	Serine/threonine kinase 32A	0.7665	76
NLGN3	Neuroligin 3	0.7660	76
SCD5	Stearoyl-CoA desaturase 5	0.7552	76
KLHL1	Kelch like family member 1	0.7415	76
CACNG4	Calcium voltage-gated channel auxiliary subunit gamma 4	0.7337	76
PLPP4	Phospholipid phosphatase 4	0.7125	76
MEGF11	Multiple EGF like domains 11	0.7086	76
EPN2	Epsin 2	0.7076	76

Adipocytes	0.3 nTPM
Breast	0.4 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	11.5 nTPM
Brain	11.5 nTPM

B-cells	0.9 nTPM
Kidney	5.2 nTPM
Lung	4.0 nTPM
Adipose tissue	2.1 nTPM
Thymus	0.4 nTPM
Salivary gland	0.3 nTPM
Spleen	0.1 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	5.8 nTPM
Endometrium	11.9 nTPM
Fallopian tube	9.5 nTPM
Lung	1.3 nTPM
Bronchus	0.3 nTPM

Club cells	0.2 nTPM
Prostate	0.3 nTPM
Bronchus	0.2 nTPM
Lung	0.1 nTPM

Endothelial cells	4.4 nTPM
Liver	22.7 nTPM
Heart muscle	19.0 nTPM
Breast	16.7 nTPM
Salivary gland	4.6 nTPM
Thymus	4.5 nTPM
Esophagus	3.6 nTPM
Vascular	2.5 nTPM
Tongue	1.6 nTPM
Fallopian tube	1.4 nTPM
Lung	0.8 nTPM
Testis	0.6 nTPM
Placenta	0.6 nTPM
Endometrium	0.4 nTPM
Skeletal muscle	0.4 nTPM
Prostate	0.3 nTPM
Skin	0.2 nTPM
Ovary	0.1 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	9.0 nTPM
Rectum	20.1 nTPM
Small intestine	6.9 nTPM
Colon	0.1 nTPM

Fibroblasts	7.5 nTPM
Adipose tissue	24.4 nTPM
Vascular	22.1 nTPM
Thymus	18.2 nTPM
Salivary gland	18.1 nTPM
Placenta	7.4 nTPM
Liver	7.1 nTPM
Heart muscle	6.7 nTPM
Prostate	4.6 nTPM
Breast	3.2 nTPM
Skeletal muscle	3.1 nTPM
Stomach	2.9 nTPM
Esophagus	1.1 nTPM
Pancreas	0.7 nTPM
Skin	0.6 nTPM
Fallopian tube	0.2 nTPM
Lung	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
Rectum	0.1 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	30.0 nTPM
Ovary	32.7 nTPM
Fallopian tube	27.3 nTPM

Macrophages	0.4 nTPM
Breast	1.3 nTPM
Testis	1.2 nTPM
Endometrium	1.2 nTPM
Vascular	1.2 nTPM
Salivary gland	0.9 nTPM
Thymus	0.4 nTPM
Fallopian tube	0.3 nTPM
Skeletal muscle	0.2 nTPM
Tongue	0.2 nTPM
Adipose tissue	0.1 nTPM
Lung	0.1 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM

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

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Cone photoreceptor cells	8.5 nTPM
Eye	8.5 nTPM

Cytotrophoblasts	22.9 nTPM
Placenta	22.9 nTPM

Early spermatids	2.7 nTPM
Testis	2.7 nTPM

Plasma cells	17.9 nTPM
Fallopian tube	70.4 nTPM
Esophagus	31.2 nTPM
Stomach	19.7 nTPM
Salivary gland	13.4 nTPM
Liver	6.0 nTPM
Bone marrow	1.5 nTPM
Thymus	0.8 nTPM
Spleen	0.2 nTPM

Schwann cells	3.1 nTPM
Vascular	7.8 nTPM
Adipose tissue	1.6 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	2.0 nTPM
Salivary gland	4.0 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.8 nTPM
Vascular	14.3 nTPM
Salivary gland	10.2 nTPM
Thymus	9.1 nTPM
Placenta	4.6 nTPM
Adipose tissue	2.2 nTPM
Liver	2.1 nTPM
Tongue	0.9 nTPM
Prostate	0.6 nTPM
Fallopian tube	0.5 nTPM
Endometrium	0.3 nTPM
Skin	0.3 nTPM
Breast	0.2 nTPM
Skeletal muscle	0.1 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.2 nTPM
Liver	1.1 nTPM
Endometrium	0.5 nTPM
Skin	0.4 nTPM
Skeletal muscle	0.4 nTPM
Prostate	0.4 nTPM
Vascular	0.4 nTPM
Breast	0.3 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	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
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM

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

Amygdala excitatory	14.3 nTPM
Thalamus	61.3 nTPM
Basal ganglia	10.9 nTPM
Hypothalamus	7.3 nTPM
Amygdala	2.2 nTPM
Hippocampus	2.0 nTPM
Cerebral cortex	1.8 nTPM

Astrocyte	136.6 nTPM
Cerebellum	578.9 nTPM
Medulla oblongata	177.6 nTPM
Pons	168.2 nTPM
Spinal cord	163.7 nTPM
Midbrain	136.7 nTPM
Basal ganglia	66.8 nTPM
Thalamus	64.7 nTPM
Hippocampus	55.3 nTPM
Hypothalamus	42.8 nTPM
Amygdala	32.5 nTPM
Cerebral cortex	15.4 nTPM

Bergmann glia	4.5 nTPM
Pons	7.2 nTPM
Cerebellum	4.1 nTPM
Medulla oblongata	2.1 nTPM

Central nervous system macrophage	3.5 nTPM
Cerebellum	7.1 nTPM
Spinal cord	6.2 nTPM
Midbrain	5.1 nTPM
Hippocampus	4.7 nTPM
Pons	3.8 nTPM
Amygdala	2.9 nTPM
Cerebral cortex	2.2 nTPM
Medulla oblongata	1.9 nTPM
Basal ganglia	1.8 nTPM
Thalamus	1.8 nTPM
Hypothalamus	0.9 nTPM

Cerebellar inhibitory	2.3 nTPM
Pons	3.5 nTPM
Spinal cord	2.7 nTPM
Midbrain	2.5 nTPM
Cerebellum	1.7 nTPM
Medulla oblongata	1.3 nTPM

Cge interneuron	69.9 nTPM
Hypothalamus	111.9 nTPM
Basal ganglia	96.4 nTPM
Amygdala	69.7 nTPM
Hippocampus	67.0 nTPM
Cerebral cortex	61.9 nTPM
Midbrain	46.6 nTPM
Thalamus	35.7 nTPM

Choroid plexus epithelial cell	4.2 nTPM
Thalamus	13.7 nTPM
Basal ganglia	1.9 nTPM
Medulla oblongata	1.0 nTPM
Hippocampus	0.0 nTPM

Committed oligodendrocyte precursor	1125.6 nTPM
Spinal cord	1913.2 nTPM
Hippocampus	1757.1 nTPM
Cerebellum	1612.5 nTPM
Midbrain	1568.3 nTPM
Cerebral cortex	1254.0 nTPM
Pons	1066.8 nTPM
Amygdala	906.7 nTPM
Basal ganglia	767.1 nTPM
Medulla oblongata	688.1 nTPM
Hypothalamus	591.3 nTPM
Thalamus	256.6 nTPM

Deep-layer corticothalamic and 6b	14.5 nTPM
Hypothalamus	19.9 nTPM
Midbrain	18.9 nTPM
Basal ganglia	16.6 nTPM
Cerebral cortex	12.7 nTPM
Amygdala	11.3 nTPM
Hippocampus	7.5 nTPM

Deep-layer intratelencephalic	1.8 nTPM
Hypothalamus	3.4 nTPM
Amygdala	1.6 nTPM
Basal ganglia	1.6 nTPM
Cerebral cortex	1.3 nTPM
Hippocampus	1.1 nTPM

Deep-layer near-projecting	1.0 nTPM
Basal ganglia	1.6 nTPM
Hypothalamus	1.5 nTPM
Amygdala	0.9 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.3 nTPM

Eccentric medium spiny neuron	1.5 nTPM
Hippocampus	2.1 nTPM
Basal ganglia	2.0 nTPM
Thalamus	1.6 nTPM
Cerebral cortex	1.4 nTPM
Hypothalamus	1.1 nTPM
Amygdala	1.0 nTPM

Endothelial cell	5.3 nTPM
Basal ganglia	12.1 nTPM
Spinal cord	12.1 nTPM
Medulla oblongata	7.2 nTPM
Hippocampus	7.1 nTPM
Cerebral cortex	6.4 nTPM
Cerebellum	3.1 nTPM
Pons	3.1 nTPM
Midbrain	2.8 nTPM
Hypothalamus	2.5 nTPM
Amygdala	1.1 nTPM
Thalamus	0.6 nTPM

Ependymal cell	460.0 nTPM
Basal ganglia	670.4 nTPM
Amygdala	586.4 nTPM
Pons	475.0 nTPM
Medulla oblongata	465.2 nTPM
Hippocampus	460.4 nTPM
Midbrain	448.2 nTPM
Spinal cord	373.7 nTPM
Hypothalamus	339.1 nTPM
Thalamus	321.9 nTPM