Single cell type - CCM2 - The Human Protein Atlas

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.	CCM2
Gene descriptionⁱ Full gene name according to HGNC.	CCM2 scaffold protein
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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. Read more	Monocytes - Immune response regulation (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. Read more	Cell type enhanced (monocytes)
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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (monocytes)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

CCM2 is part of cluster 3 Monocytes - Immune response regulation with confidenceⁱ 1
114 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
DOK1	Docking protein 1	0.7242	4
ARPC4	Actin related protein 2/3 complex subunit 4	0.7139	3
DBNL	Drebrin like	0.7139	3
MYO1G	Myosin IG	0.7109	3
TWF2	Twinfilin actin binding protein 2	0.6786	3
GPSM3	G protein signaling modulator 3	0.6603	63
LSP1	Lymphocyte specific protein 1	0.6481	3
DDB2	Damage specific DNA binding protein 2	0.6336	3
TYMP	Thymidine phosphorylase	0.6272	3
CCL17	C-C motif chemokine ligand 17	0.6215	3
SNX11	Sorting nexin 11	0.6194	3
IL12B	Interleukin 12B	0.6189	3
CCL22	C-C motif chemokine ligand 22	0.6176	3
SHKBP1	SH3KBP1 binding protein 1	0.6170	3
FOXD4L1	Forkhead box D4 like 1	0.6100	3

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	28.7 nTPM
Breast	30.9 nTPM
Adipose tissue	26.6 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	19.4 nTPM
Lung	19.4 nTPM

Astrocytes	26.1 nTPM
Brain	26.1 nTPM

B-cells	57.5 nTPM
Kidney	114.3 nTPM
PBMC	105.6 nTPM
Liver	75.8 nTPM
Breast	66.9 nTPM
Bone marrow	53.2 nTPM
Lymph node	49.6 nTPM
Spleen	42.2 nTPM
Colon	25.5 nTPM
Stomach	22.3 nTPM
Adipose tissue	19.5 nTPM

Dendritic cells	53.7 nTPM
Breast	67.0 nTPM
Adipose tissue	66.2 nTPM
PBMC	27.9 nTPM

Endothelial cells	26.7 nTPM
Ovary	47.5 nTPM
Liver	41.2 nTPM
Eye	33.2 nTPM
Testis	32.0 nTPM
Skin	31.2 nTPM
Placenta	30.7 nTPM
Skeletal muscle	27.2 nTPM
Prostate	23.7 nTPM
Breast	20.7 nTPM
Esophagus	19.6 nTPM
Pancreas	19.3 nTPM
Endometrium	17.9 nTPM
Lung	15.6 nTPM
Heart muscle	14.1 nTPM

Fibroblasts	25.0 nTPM
Ovary	38.2 nTPM
Skin	34.8 nTPM
Breast	30.2 nTPM
Adipose tissue	28.9 nTPM
Placenta	28.1 nTPM
Stomach	26.7 nTPM
Skeletal muscle	26.1 nTPM
Prostate	19.8 nTPM
Lung	19.0 nTPM
Esophagus	16.0 nTPM
Heart muscle	7.2 nTPM

Intestinal goblet cells	15.2 nTPM
Colon	16.5 nTPM
Rectum	15.4 nTPM
Small intestine	13.6 nTPM

Macrophages	47.7 nTPM
Pancreas	91.9 nTPM
PBMC	68.2 nTPM
Ovary	64.3 nTPM
Kidney	60.5 nTPM
Testis	52.9 nTPM
Bone marrow	52.4 nTPM
Breast	48.6 nTPM
Esophagus	44.1 nTPM
Prostate	43.5 nTPM
Adipose tissue	41.2 nTPM
Lung	35.8 nTPM
Skeletal muscle	34.9 nTPM
Spleen	30.0 nTPM
Stomach	26.4 nTPM
Endometrium	20.5 nTPM

Paneth cells	11.4 nTPM
Rectum	17.2 nTPM
Colon	13.2 nTPM
Small intestine	3.7 nTPM

Plasma cells	69.1 nTPM
Esophagus	86.2 nTPM
Adipose tissue	74.9 nTPM
Spleen	71.8 nTPM
Bone marrow	59.4 nTPM
Stomach	53.1 nTPM

Respiratory ciliated cells	8.0 nTPM
Bronchus	8.9 nTPM
Lung	7.3 nTPM

Smooth muscle cells	29.6 nTPM
Pancreas	80.8 nTPM
Ovary	53.6 nTPM
Skin	35.3 nTPM
Prostate	27.2 nTPM
Breast	26.8 nTPM
Adipose tissue	23.6 nTPM
Skeletal muscle	21.4 nTPM
Endometrium	20.5 nTPM
Heart muscle	14.0 nTPM
Esophagus	14.0 nTPM
Bronchus	8.4 nTPM

T-cells	55.7 nTPM
Ovary	100.1 nTPM
PBMC	90.1 nTPM
Liver	83.6 nTPM
Kidney	80.1 nTPM
Adipose tissue	65.6 nTPM
Breast	62.8 nTPM
Skin	62.7 nTPM
Skeletal muscle	58.4 nTPM
Bone marrow	52.5 nTPM
Lymph node	49.2 nTPM
Lung	44.0 nTPM
Colon	42.7 nTPM
Spleen	39.8 nTPM
Prostate	37.9 nTPM
Endometrium	29.5 nTPM
Stomach	28.4 nTPM
Esophagus	19.7 nTPM

Basal keratinocytes	46.8 nTPM
Skin	46.8 nTPM

Basal prostatic cells	22.6 nTPM
Prostate	22.6 nTPM

Basal respiratory cells	27.6 nTPM
Bronchus	27.6 nTPM

Basal squamous epithelial cells	54.7 nTPM
Esophagus	54.7 nTPM

Undifferentiated cells	15.2 nTPM
Colon	16.1 nTPM
Rectum	15.2 nTPM
Small intestine	14.3 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC