Single cell type - RUNX3 - 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.	RUNX3
Gene descriptionⁱ Full gene name according to HGNC.	RUNX family transcription factor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transcription factors
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.	3

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	Non-specific - Transcription 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 (dendritic cells, NK-cells, T-cells, Langerhans cells, 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	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 many
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 (HDLM-2, Karpas-707, SK-MEL-30, U-266/70)
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 (dendritic cells, NK-cells, T-cells, Langerhans cells, 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

RUNX3 is part of cluster 24 Non-specific - Transcription regulation with confidenceⁱ 1
415 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
PPP2R5C	Protein phosphatase 2 regulatory subunit B'gamma	0.8812	24
GZMK	Granzyme K	0.8427	24
RNF125	Ring finger protein 125	0.8381	24
CRTAM	Cytotoxic and regulatory T cell molecule	0.8322	24
MYBL1	MYB proto-oncogene like 1	0.8226	24
XCL1	X-C motif chemokine ligand 1	0.8159	63
SHISAL2A	Shisa like 2A	0.7940	7
SYTL3	Synaptotagmin like 3	0.7836	24
XCL2	X-C motif chemokine ligand 2	0.7801	63
PTPN22	Protein tyrosine phosphatase non-receptor type 22	0.7790	24
CNOT6L	CCR4-NOT transcription complex subunit 6 like	0.7723	24
SLA	Src like adaptor	0.7678	24
CEMIP2	Cell migration inducing hyaluronidase 2	0.7601	24
CCL4	C-C motif chemokine ligand 4	0.7598	63
IL18RAP	Interleukin 18 receptor accessory protein	0.7593	63

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	4.4 nTPM
Breast	7.0 nTPM
Adipose tissue	1.9 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	3.6 nTPM
Lung	3.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	57.7 nTPM
Colon	103.8 nTPM
Adipose tissue	98.3 nTPM
Lymph node	67.1 nTPM
Stomach	60.0 nTPM
Breast	54.9 nTPM
Spleen	53.6 nTPM
PBMC	45.7 nTPM
Kidney	38.1 nTPM
Bone marrow	30.2 nTPM
Liver	25.2 nTPM

Dendritic cells	336.4 nTPM
Adipose tissue	649.8 nTPM
Breast	351.3 nTPM
PBMC	8.0 nTPM

Endothelial cells	2.4 nTPM
Skin	14.0 nTPM
Pancreas	3.9 nTPM
Breast	3.8 nTPM
Liver	3.7 nTPM
Esophagus	2.6 nTPM
Endometrium	1.9 nTPM
Heart muscle	1.7 nTPM
Skeletal muscle	1.5 nTPM
Placenta	0.6 nTPM
Prostate	0.1 nTPM
Eye	0.0 nTPM
Lung	0.0 nTPM
Testis	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	3.3 nTPM
Skin	14.0 nTPM
Stomach	10.4 nTPM
Breast	5.9 nTPM
Esophagus	1.8 nTPM
Placenta	1.3 nTPM
Skeletal muscle	1.2 nTPM
Prostate	0.7 nTPM
Heart muscle	0.5 nTPM
Adipose tissue	0.4 nTPM
Ovary	0.1 nTPM
Lung	0.0 nTPM

Intestinal goblet cells	0.5 nTPM
Colon	1.4 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	55.6 nTPM
Breast	145.1 nTPM
Prostate	136.5 nTPM
Endometrium	136.0 nTPM
Adipose tissue	84.5 nTPM
Esophagus	61.4 nTPM
Spleen	57.0 nTPM
Pancreas	48.5 nTPM
Skeletal muscle	42.7 nTPM
Bone marrow	35.0 nTPM
Kidney	26.5 nTPM
Lung	23.8 nTPM
Stomach	23.5 nTPM
Ovary	10.8 nTPM
Testis	3.5 nTPM
PBMC	0.0 nTPM

Paneth cells	0.1 nTPM
Rectum	0.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	87.1 nTPM
Adipose tissue	373.6 nTPM
Spleen	18.6 nTPM
Bone marrow	16.5 nTPM
Stomach	14.4 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	0.5 nTPM
Bronchus	1.0 nTPM
Lung	0.0 nTPM

Smooth muscle cells	3.6 nTPM
Breast	12.8 nTPM
Skin	8.7 nTPM
Prostate	5.3 nTPM
Esophagus	4.6 nTPM
Endometrium	3.0 nTPM
Adipose tissue	1.8 nTPM
Skeletal muscle	1.6 nTPM
Bronchus	0.9 nTPM
Heart muscle	0.5 nTPM
Pancreas	0.1 nTPM
Ovary	0.1 nTPM

T-cells	215.4 nTPM
Adipose tissue	582.6 nTPM
Endometrium	401.6 nTPM
Skeletal muscle	355.2 nTPM
Breast	320.4 nTPM
Colon	284.2 nTPM
Ovary	238.0 nTPM
Stomach	215.3 nTPM
Skin	207.7 nTPM
Esophagus	190.0 nTPM
Spleen	170.6 nTPM
Liver	161.5 nTPM
Lymph node	148.1 nTPM
PBMC	95.4 nTPM
Bone marrow	84.7 nTPM
Kidney	71.8 nTPM
Prostate	71.1 nTPM
Lung	63.8 nTPM

Basal keratinocytes	7.6 nTPM
Skin	7.6 nTPM

Basal prostatic cells	0.8 nTPM
Prostate	0.8 nTPM

Basal squamous epithelial cells	2.2 nTPM
Esophagus	2.2 nTPM

Early spermatids	2.3 nTPM
Testis	2.3 nTPM

Undifferentiated cells	0.4 nTPM
Colon	1.0 nTPM
Rectum	0.1 nTPM
Small intestine	0.0 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