Single cell type - CITED4 - 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.	CITED4
Gene descriptionⁱ Full gene name according to HGNC.	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4
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.	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. Read more	Endometrium - Transcription (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 (Endometrial ciliated cells, Cholangiocytes, Breast myoepithelial cells, Glandular and luminal cells, Breast glandular cells, Basal prostatic 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	Not detected in immune cells
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	Not detected
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 (RPTEC TERT1, THP-1)
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 (Endometrial ciliated cells, Cholangiocytes, Breast myoepithelial cells, Glandular and luminal cells, Breast glandular cells, Basal prostatic 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

CITED4 is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
TESMIN	Testis expressed metallothionein like protein	0.7567	44
SCGB1D2	Secretoglobin family 1D member 2	0.6788	44
FAM110C	Family with sequence similarity 110 member C	0.6654	22
SPINT3	Serine peptidase inhibitor, Kunitz type 3	0.6561	44
LPAR3	Lysophosphatidic acid receptor 3	0.6429	44
MSX1	Msh homeobox 1	0.6422	44
TMEM270	Transmembrane protein 270	0.6373	49
RNF223	Ring finger protein 223	0.6367	35
SIX4	SIX homeobox 4	0.6345	44
TENT5B	Terminal nucleotidyltransferase 5B	0.6153	35
FSBP	Fibrinogen silencer binding protein	0.6130	44
SCGB2A1	Secretoglobin family 2A member 1	0.6121	44
MAFF	MAF bZIP transcription factor F	0.6107	44
CLDN22	Claudin 22	0.6089	44
HOMER2	Homer scaffold protein 2	0.6031	44

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	17.4 nTPM
Breast	25.5 nTPM
Adipose tissue	9.3 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	1.1 nTPM
Lung	1.1 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	4.0 nTPM
Kidney	14.3 nTPM
Breast	9.4 nTPM
Adipose tissue	7.0 nTPM
Liver	4.6 nTPM
Lymph node	2.5 nTPM
Bone marrow	0.8 nTPM
Spleen	0.7 nTPM
Stomach	0.5 nTPM
Colon	0.0 nTPM
PBMC	0.0 nTPM

Dendritic cells	11.9 nTPM
Breast	27.7 nTPM
Adipose tissue	8.1 nTPM
PBMC	0.0 nTPM

Endothelial cells	48.9 nTPM
Endometrium	369.6 nTPM
Prostate	98.6 nTPM
Ovary	88.4 nTPM
Breast	50.3 nTPM
Skin	26.6 nTPM
Placenta	13.1 nTPM
Eye	12.2 nTPM
Esophagus	11.3 nTPM
Skeletal muscle	6.0 nTPM
Testis	4.1 nTPM
Liver	2.7 nTPM
Heart muscle	2.4 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	14.0 nTPM
Adipose tissue	42.6 nTPM
Prostate	24.2 nTPM
Breast	24.0 nTPM
Skeletal muscle	20.5 nTPM
Ovary	15.5 nTPM
Esophagus	8.4 nTPM
Stomach	7.4 nTPM
Heart muscle	4.7 nTPM
Skin	4.3 nTPM
Lung	2.2 nTPM
Placenta	0.5 nTPM

Intestinal goblet cells	4.8 nTPM
Colon	7.2 nTPM
Small intestine	4.3 nTPM
Rectum	3.0 nTPM

Macrophages	13.7 nTPM
Endometrium	39.3 nTPM
Prostate	29.8 nTPM
Breast	25.5 nTPM
Kidney	21.1 nTPM
Spleen	18.6 nTPM
Stomach	17.6 nTPM
Bone marrow	13.8 nTPM
Adipose tissue	11.6 nTPM
Ovary	10.0 nTPM
Skeletal muscle	8.1 nTPM
Esophagus	6.3 nTPM
Testis	3.5 nTPM
Lung	0.3 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

Paneth cells	3.4 nTPM
Small intestine	3.7 nTPM
Rectum	3.4 nTPM
Colon	3.3 nTPM

Plasma cells	2.4 nTPM
Adipose tissue	6.4 nTPM
Stomach	5.0 nTPM
Spleen	0.7 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	6.5 nTPM
Bronchus	8.6 nTPM
Lung	4.4 nTPM

Smooth muscle cells	19.7 nTPM
Ovary	45.8 nTPM
Prostate	43.7 nTPM
Breast	34.4 nTPM
Adipose tissue	24.0 nTPM
Endometrium	20.7 nTPM
Skeletal muscle	19.2 nTPM
Esophagus	15.5 nTPM
Skin	5.2 nTPM
Heart muscle	4.2 nTPM
Pancreas	2.7 nTPM
Bronchus	1.9 nTPM

T-cells	14.6 nTPM
Endometrium	48.6 nTPM
Breast	48.6 nTPM
Prostate	23.6 nTPM
Kidney	22.0 nTPM
Adipose tissue	14.8 nTPM
Lymph node	12.0 nTPM
Ovary	11.1 nTPM
Skeletal muscle	10.0 nTPM
Stomach	9.8 nTPM
Bone marrow	9.2 nTPM
PBMC	8.6 nTPM
Spleen	8.4 nTPM
Liver	8.0 nTPM
Esophagus	6.6 nTPM
Skin	3.6 nTPM
Colon	3.3 nTPM
Lung	0.0 nTPM

Cholangiocytes	258.7 nTPM
Liver	258.7 nTPM

Cytotrophoblasts	1.0 nTPM
Placenta	1.0 nTPM

Distal tubular cells	43.0 nTPM
Kidney	43.0 nTPM

Early spermatids	47.9 nTPM
Testis	47.9 nTPM

Undifferentiated cells	3.6 nTPM
Colon	5.8 nTPM
Rectum	3.2 nTPM
Small intestine	2.0 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