Single cell type - CITED2 - 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.	CITED2
Gene descriptionⁱ Full gene name according to HGNC.	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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	Plasma cells - Humoral 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. Read more	Cell type enhanced (Extravillous trophoblasts, Plasma cells)
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	Immune cell enhanced (eosinophil)
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	Cell line enhanced (BJ, fHDF/TERT166)
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 many
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 (Extravillous trophoblasts, Plasma cells)

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

CITED2 is part of cluster 55 Plasma cells - Humoral immune response with confidenceⁱ 1
379 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
GPR15	G protein-coupled receptor 15	0.6839	55
TAGAP	T cell activation RhoGTPase activating protein	0.6474	59
IGKV1D-13	Immunoglobulin kappa variable 1D-13	0.6064	55
IGLV1-50	Immunoglobulin lambda variable 1-50 (non-functional)	0.6060	55
IGHA2	Immunoglobulin heavy constant alpha 2 (A2m marker)	0.5879	55
IGKV2-28	Immunoglobulin kappa variable 2-28	0.5621	55
ERN1	Endoplasmic reticulum to nucleus signaling 1	0.5599	55
IGLV1-40	Immunoglobulin lambda variable 1-40	0.5511	55
IGHV4-4	Immunoglobulin heavy variable 4-4	0.5471	55
CALR	Calreticulin	0.5460	38
IGKV3D-20	Immunoglobulin kappa variable 3D-20	0.5396	55
IGHA1	Immunoglobulin heavy constant alpha 1	0.5360	55
IDUA	Alpha-L-iduronidase	0.5236	55
IGKV1D-39	Immunoglobulin kappa variable 1D-39	0.5190	55
IGHV3-74	Immunoglobulin heavy variable 3-74	0.5185	55

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	157.1 nTPM
Breast	222.7 nTPM
Adipose tissue	91.5 nTPM

Alveolar cells type 1	115.4 nTPM
Lung	115.4 nTPM

Alveolar cells type 2	272.8 nTPM
Lung	272.8 nTPM

Astrocytes	3.6 nTPM
Brain	3.6 nTPM

B-cells	138.8 nTPM
Lymph node	458.0 nTPM
Breast	337.0 nTPM
Liver	168.1 nTPM
Stomach	132.6 nTPM
Adipose tissue	85.7 nTPM
Spleen	59.1 nTPM
Colon	47.9 nTPM
Kidney	38.1 nTPM
PBMC	35.7 nTPM
Bone marrow	25.3 nTPM

Basal squamous epithelial cells	347.8 nTPM
Esophagus	347.8 nTPM

Dendritic cells	156.5 nTPM
Breast	307.6 nTPM
Adipose tissue	142.1 nTPM
PBMC	20.0 nTPM

Endothelial cells	68.9 nTPM
Esophagus	236.0 nTPM
Breast	182.0 nTPM
Skin	98.2 nTPM
Skeletal muscle	77.6 nTPM
Liver	67.8 nTPM
Prostate	58.9 nTPM
Endometrium	53.1 nTPM
Placenta	47.2 nTPM
Eye	43.7 nTPM
Testis	31.4 nTPM
Ovary	26.7 nTPM
Heart muscle	17.2 nTPM
Pancreas	15.5 nTPM
Lung	9.3 nTPM

Enteroendocrine cells	99.7 nTPM
Rectum	114.1 nTPM
Colon	85.3 nTPM

Erythroid cells	274.3 nTPM
Liver	438.4 nTPM
Bone marrow	110.1 nTPM

Fibroblasts	200.3 nTPM
Placenta	549.5 nTPM
Esophagus	542.9 nTPM
Adipose tissue	311.5 nTPM
Stomach	262.8 nTPM
Breast	203.4 nTPM
Skeletal muscle	90.0 nTPM
Skin	57.8 nTPM
Heart muscle	56.2 nTPM
Prostate	54.8 nTPM
Ovary	48.2 nTPM
Lung	25.7 nTPM

Intestinal goblet cells	111.6 nTPM
Rectum	138.9 nTPM
Colon	125.0 nTPM
Small intestine	70.7 nTPM

Macrophages	188.9 nTPM
Breast	554.2 nTPM
Esophagus	464.2 nTPM
Stomach	339.9 nTPM
Adipose tissue	226.5 nTPM
Testis	212.6 nTPM
Prostate	166.3 nTPM
Ovary	159.9 nTPM
Lung	154.7 nTPM
Endometrium	134.0 nTPM
Spleen	133.8 nTPM
Skeletal muscle	114.0 nTPM
Kidney	65.8 nTPM
Bone marrow	61.2 nTPM
Pancreas	46.0 nTPM
PBMC	0.0 nTPM

Paneth cells	97.7 nTPM
Rectum	127.3 nTPM
Small intestine	90.1 nTPM
Colon	75.8 nTPM

Plasma cells	619.4 nTPM
Stomach	1449.6 nTPM
Esophagus	991.5 nTPM
Spleen	311.1 nTPM
Bone marrow	178.0 nTPM
Adipose tissue	167.0 nTPM

Cholangiocytes	80.1 nTPM
Liver	80.1 nTPM

Collecting duct cells	103.0 nTPM
Kidney	103.0 nTPM

Cone photoreceptor cells	12.5 nTPM
Eye	12.5 nTPM

Cytotrophoblasts	173.1 nTPM
Placenta	173.1 nTPM

Respiratory ciliated cells	27.4 nTPM
Bronchus	28.7 nTPM
Lung	26.2 nTPM

Smooth muscle cells	179.1 nTPM
Ovary	565.8 nTPM
Esophagus	286.9 nTPM
Skeletal muscle	286.7 nTPM
Adipose tissue	265.1 nTPM
Breast	170.3 nTPM
Skin	106.2 nTPM
Endometrium	84.7 nTPM
Prostate	65.0 nTPM
Pancreas	57.7 nTPM
Bronchus	50.3 nTPM
Heart muscle	31.8 nTPM

T-cells	291.8 nTPM
Lymph node	793.1 nTPM
Breast	685.0 nTPM
Stomach	517.2 nTPM
Adipose tissue	350.1 nTPM
Ovary	340.4 nTPM
Esophagus	294.8 nTPM
Skin	293.8 nTPM
Prostate	293.5 nTPM
Spleen	270.9 nTPM
Endometrium	253.6 nTPM
Skeletal muscle	194.8 nTPM
Liver	183.5 nTPM
Colon	149.7 nTPM
Kidney	132.8 nTPM
Bone marrow	75.2 nTPM
Lung	66.8 nTPM
PBMC	64.7 nTPM

Undifferentiated cells	112.6 nTPM
Rectum	135.3 nTPM
Small intestine	108.8 nTPM
Colon	93.6 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