Single cell type - CCN3 - The Human Protein Atlas

CCN3

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Pathway

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.	CCN3
Gene descriptionⁱ Full gene name according to HGNC.	Cellular communication network factor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma proteins Transporters
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.	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.	Smooth muscle cells - Muscle contraction (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 (Melanocytes, Granulocytes, Smooth muscle cells, Glandular and luminal cells, Fibroblasts)
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.	0.71
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.	Group enriched (eosinophil, neutrophil)
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 (Melanocytes, Granulocytes, Smooth muscle cells, Glandular and luminal cells, Fibroblasts)

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: Group enriched (eosinophil, neutrophil)
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

CCN3 is part of cluster 32 Smooth muscle cells - Muscle contraction with confidenceⁱ 1
236 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.
BGN	Biglycan	0.8421	32
LTBP2	Latent transforming growth factor beta binding protein 2	0.8415	32
CRLF1	Cytokine receptor like factor 1	0.8388	32
COL8A1	Collagen type VIII alpha 1 chain	0.8136	32
LTBP1	Latent transforming growth factor beta binding protein 1	0.8081	32
COL14A1	Collagen type XIV alpha 1 chain	0.8043	32
ITGA11	Integrin subunit alpha 11	0.7944	53
MYH11	Myosin heavy chain 11	0.7881	32
COMP	Cartilage oligomeric matrix protein	0.7855	32
ITGBL1	Integrin subunit beta like 1	0.7782	32
AEBP1	AE binding protein 1	0.7762	32
SCUBE3	Signal peptide, CUB domain and EGF like domain containing 3	0.7720	32
ELN	Elastin	0.7660	32
ENSG00000285868	Novel protein	0.7624	32
ITGA8	Integrin subunit alpha 8	0.7547	32

IMMUNE CELLS

CCN3 is part of cluster 36 Eosinophils - Protein ubiquitination with confidenceⁱ 0.99
179 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.
PPARD	Peroxisome proliferator activated receptor delta	0.9762	36
DNAJA4	DnaJ heat shock protein family (Hsp40) member A4	0.9762	36
CDAN1	Codanin 1	0.9762	36
ITGB7	Integrin subunit beta 7	0.9762	36
BLTP1	Bridge-like lipid transfer protein family member 1	0.9762	36
ANKRD6	Ankyrin repeat domain 6	0.9762	36
C9orf40	Chromosome 9 open reading frame 40	0.9762	36
DSC2	Desmocollin 2	0.9762	36
GADD45G	Growth arrest and DNA damage inducible gamma	0.9762	36
TUSC2	Tumor suppressor 2, mitochondrial calcium regulator	0.9762	19
AOC1	Amine oxidase copper containing 1	0.9762	36
KRT23	Keratin 23	0.9762	36
OLFM2	Olfactomedin 2	0.9762	36
MAPK3	Mitogen-activated protein kinase 3	0.9762	36
TTI1	TELO2 interacting protein 1	0.9762	36

Adipocytes	35.9 nTPM
Adipose tissue	47.3 nTPM
Breast	24.6 nTPM

Alveolar cells type 1	0.1 nTPM
Lung	0.1 nTPM

Alveolar cells type 2	0.9 nTPM
Lung	0.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	1.3 nTPM
Skin	8.5 nTPM
Esophagus	5.9 nTPM
Thymus	2.1 nTPM
Salivary gland	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	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

Ciliated cells	11.4 nTPM
Endometrium	32.9 nTPM
Fallopian tube	10.0 nTPM
Lung	2.6 nTPM
Bronchus	0.2 nTPM

Club cells	1.2 nTPM
Prostate	2.3 nTPM
Lung	1.2 nTPM
Bronchus	0.1 nTPM

Endothelial cells	14.7 nTPM
Salivary gland	55.3 nTPM
Ovary	27.4 nTPM
Heart muscle	22.1 nTPM
Prostate	20.7 nTPM
Skeletal muscle	19.1 nTPM
Endometrium	18.9 nTPM
Esophagus	17.2 nTPM
Vascular	14.1 nTPM
Placenta	13.6 nTPM
Thymus	13.4 nTPM
Fallopian tube	13.3 nTPM
Tongue	12.3 nTPM
Testis	6.1 nTPM
Lung	4.9 nTPM
Skin	4.3 nTPM
Breast	1.8 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	12.3 nTPM
Colon	21.8 nTPM
Rectum	11.7 nTPM
Small intestine	3.4 nTPM

Fibroblasts	45.1 nTPM
Skeletal muscle	418.1 nTPM
Heart muscle	85.8 nTPM
Skin	67.7 nTPM
Adipose tissue	57.9 nTPM
Vascular	36.8 nTPM
Salivary gland	10.7 nTPM
Fallopian tube	10.6 nTPM
Stomach	10.1 nTPM
Thymus	8.6 nTPM
Breast	7.4 nTPM
Lung	2.9 nTPM
Esophagus	2.4 nTPM
Prostate	1.3 nTPM
Pancreas	0.9 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM

Granulocytes	82.3 nTPM
Fallopian tube	162.0 nTPM
Tongue	58.2 nTPM
Lung	26.7 nTPM

Intestinal goblet cells	4.8 nTPM
Colon	8.4 nTPM
Rectum	6.0 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	6.9 nTPM
Fallopian tube	13.8 nTPM
Ovary	0.0 nTPM

Macrophages	4.0 nTPM
Vascular	19.9 nTPM
Skin	13.4 nTPM
Thymus	11.3 nTPM
Endometrium	7.4 nTPM
Esophagus	5.1 nTPM
Skeletal muscle	4.2 nTPM
Tongue	2.8 nTPM
Adipose tissue	2.3 nTPM
Salivary gland	2.3 nTPM
Breast	2.3 nTPM
Lung	1.6 nTPM
Fallopian tube	1.1 nTPM
Kidney	0.9 nTPM
Prostate	0.9 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	10.1 nTPM
Colon	18.1 nTPM
Rectum	8.7 nTPM
Small intestine	3.5 nTPM

Basal respiratory cells	0.3 nTPM
Bronchus	0.3 nTPM

Basal squamous epithelial cells	3.3 nTPM
Esophagus	3.3 nTPM

Collecting duct cells	31.1 nTPM
Kidney	31.1 nTPM

Endometrial stromal cells	35.3 nTPM
Endometrium	35.3 nTPM

Plasma cells	0.3 nTPM
Salivary gland	0.9 nTPM
Thymus	0.7 nTPM
Fallopian tube	0.6 nTPM
Liver	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	30.0 nTPM
Vascular	86.2 nTPM
Adipose tissue	3.9 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	0.3 nTPM
Salivary gland	0.5 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	72.1 nTPM
Vascular	533.3 nTPM
Thymus	367.8 nTPM
Prostate	61.4 nTPM
Salivary gland	47.0 nTPM
Fallopian tube	31.2 nTPM
Breast	29.4 nTPM
Skin	20.9 nTPM
Ovary	14.6 nTPM
Lung	12.9 nTPM
Skeletal muscle	8.6 nTPM
Endometrium	8.4 nTPM
Placenta	6.2 nTPM
Tongue	4.8 nTPM
Esophagus	3.6 nTPM
Adipose tissue	2.7 nTPM
Liver	1.3 nTPM

T-cells	1.8 nTPM
Vascular	23.7 nTPM
Endometrium	6.5 nTPM
Skeletal muscle	2.3 nTPM
Skin	1.4 nTPM
Colon	1.0 nTPM
Tongue	0.9 nTPM
Breast	0.6 nTPM
Liver	0.3 nTPM
Lymph node	0.2 nTPM
Prostate	0.2 nTPM
Salivary gland	0.2 nTPM
Fallopian tube	0.2 nTPM
Stomach	0.1 nTPM
Thymus	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
Lung	0.0 nTPM

Undifferentiated cells	13.9 nTPM
Colon	24.7 nTPM
Rectum	16.1 nTPM
Small intestine	1.0 nTPM

Amygdala excitatory	9.0 nTPM
Basal ganglia	21.6 nTPM
Hypothalamus	10.0 nTPM
Hippocampus	8.3 nTPM
Cerebral cortex	5.4 nTPM
Thalamus	4.5 nTPM
Amygdala	4.4 nTPM

Astrocyte	0.5 nTPM
Cerebral cortex	1.1 nTPM
Hypothalamus	1.1 nTPM
Hippocampus	1.0 nTPM
Spinal cord	0.5 nTPM
Amygdala	0.4 nTPM
Medulla oblongata	0.4 nTPM
Midbrain	0.3 nTPM
Thalamus	0.3 nTPM
Basal ganglia	0.1 nTPM
Cerebellum	0.0 nTPM
Pons	0.0 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.7 nTPM
Hippocampus	2.1 nTPM
Cerebral cortex	1.8 nTPM
Hypothalamus	1.6 nTPM
Amygdala	0.6 nTPM
Medulla oblongata	0.5 nTPM
Spinal cord	0.3 nTPM
Thalamus	0.3 nTPM
Cerebellum	0.1 nTPM
Midbrain	0.1 nTPM
Pons	0.1 nTPM
Basal ganglia	0.0 nTPM

Cerebellar inhibitory	0.9 nTPM
Pons	1.7 nTPM
Midbrain	1.2 nTPM
Medulla oblongata	1.1 nTPM
Cerebellum	0.5 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	14.2 nTPM
Midbrain	21.3 nTPM
Thalamus	20.8 nTPM
Basal ganglia	13.3 nTPM
Hippocampus	12.0 nTPM
Cerebral cortex	11.7 nTPM
Amygdala	10.9 nTPM
Hypothalamus	9.3 nTPM

Choroid plexus epithelial cell	0.3 nTPM
Medulla oblongata	0.7 nTPM
Basal ganglia	0.4 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	1.5 nTPM
Pons	5.3 nTPM
Hypothalamus	2.0 nTPM
Cerebral cortex	1.9 nTPM
Amygdala	1.7 nTPM
Cerebellum	1.6 nTPM
Hippocampus	1.3 nTPM
Medulla oblongata	1.3 nTPM
Basal ganglia	1.1 nTPM
Thalamus	0.2 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	11.6 nTPM
Amygdala	13.8 nTPM
Hippocampus	13.6 nTPM
Hypothalamus	12.3 nTPM
Midbrain	12.2 nTPM
Basal ganglia	11.4 nTPM
Cerebral cortex	6.6 nTPM

Deep-layer intratelencephalic	12.1 nTPM
Hypothalamus	14.4 nTPM
Basal ganglia	14.2 nTPM
Hippocampus	12.0 nTPM
Cerebral cortex	11.0 nTPM
Amygdala	8.7 nTPM

Deep-layer near-projecting	12.0 nTPM
Basal ganglia	17.3 nTPM
Hypothalamus	12.8 nTPM
Hippocampus	12.0 nTPM
Cerebral cortex	8.9 nTPM
Amygdala	8.7 nTPM

Eccentric medium spiny neuron	2.0 nTPM
Hypothalamus	3.3 nTPM
Hippocampus	2.5 nTPM
Thalamus	1.8 nTPM
Cerebral cortex	1.7 nTPM
Basal ganglia	1.6 nTPM
Amygdala	1.2 nTPM

Endothelial cell	17.2 nTPM
Cerebellum	27.1 nTPM
Basal ganglia	26.1 nTPM
Pons	25.6 nTPM
Medulla oblongata	24.6 nTPM
Thalamus	24.3 nTPM
Spinal cord	17.3 nTPM
Midbrain	13.2 nTPM
Cerebral cortex	10.2 nTPM
Hippocampus	9.6 nTPM
Hypothalamus	8.7 nTPM
Amygdala	2.2 nTPM

Ependymal cell	3.6 nTPM
Spinal cord	5.7 nTPM
Medulla oblongata	5.3 nTPM
Midbrain	5.1 nTPM
Pons	4.7 nTPM
Hypothalamus	4.5 nTPM
Hippocampus	2.4 nTPM
Thalamus	2.0 nTPM
Basal ganglia	1.5 nTPM
Amygdala	1.1 nTPM