Single cell type - KDM4A - 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.	KDM4A
Gene descriptionⁱ Full gene name according to HGNC.	Lysine demethylase 4A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	2

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 (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	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. 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: Low cell type specificity

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

KDM4A is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
DIABLO	Diablo IAP-binding mitochondrial protein	0.5217	59
NHEJ1	Non-homologous end joining factor 1	0.5181	59
USP19	Ubiquitin specific peptidase 19	0.5166	10
FCHSD1	FCH and double SH3 domains 1	0.4919	58
RAVER1	Ribonucleoprotein, PTB binding 1	0.4771	59
ZNF740	Zinc finger protein 740	0.4725	59
DPH1	Diphthamide biosynthesis 1	0.4599	59
ALG11	ALG11 alpha-1,2-mannosyltransferase	0.4581	59
TRIM34	Tripartite motif containing 34	0.4546	59
CBWD5	COBW domain containing 5	0.4511	59
ST20-MTHFS	ST20-MTHFS readthrough	0.4470	59
PGAP3	Post-GPI attachment to proteins phospholipase 3	0.4452	53
GET4	Guided entry of tail-anchored proteins factor 4	0.4387	59
SLC35E2B	Solute carrier family 35 member E2B	0.4380	9
ZNF484	Zinc finger protein 484	0.4377	59

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	5.3 nTPM
Breast	6.2 nTPM
Adipose tissue	4.5 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	22.3 nTPM
Lung	22.3 nTPM

Astrocytes	12.7 nTPM
Brain	12.7 nTPM

B-cells	14.0 nTPM
Bone marrow	31.1 nTPM
Stomach	24.1 nTPM
Lymph node	22.0 nTPM
Spleen	19.7 nTPM
PBMC	15.7 nTPM
Breast	9.4 nTPM
Liver	7.1 nTPM
Adipose tissue	6.0 nTPM
Colon	4.8 nTPM
Kidney	0.0 nTPM

Dendritic cells	10.4 nTPM
PBMC	20.0 nTPM
Adipose tissue	7.3 nTPM
Breast	4.0 nTPM

Endothelial cells	9.2 nTPM
Heart muscle	16.5 nTPM
Eye	15.4 nTPM
Liver	13.7 nTPM
Testis	13.0 nTPM
Esophagus	11.8 nTPM
Pancreas	11.6 nTPM
Skeletal muscle	10.5 nTPM
Endometrium	8.7 nTPM
Ovary	6.5 nTPM
Breast	6.3 nTPM
Placenta	5.7 nTPM
Skin	5.2 nTPM
Prostate	3.3 nTPM
Lung	0.0 nTPM

Fibroblasts	9.8 nTPM
Esophagus	14.9 nTPM
Stomach	14.9 nTPM
Skeletal muscle	12.1 nTPM
Heart muscle	11.7 nTPM
Placenta	11.6 nTPM
Lung	10.1 nTPM
Breast	9.9 nTPM
Ovary	7.3 nTPM
Adipose tissue	7.2 nTPM
Skin	4.7 nTPM
Prostate	3.1 nTPM

Intestinal goblet cells	16.6 nTPM
Rectum	23.4 nTPM
Small intestine	17.1 nTPM
Colon	9.3 nTPM

Macrophages	7.9 nTPM
Stomach	14.7 nTPM
Skeletal muscle	13.1 nTPM
Pancreas	10.2 nTPM
Ovary	10.0 nTPM
Bone marrow	10.0 nTPM
Testis	9.8 nTPM
Esophagus	9.4 nTPM
Spleen	9.3 nTPM
Lung	8.3 nTPM
Breast	6.0 nTPM
Prostate	5.7 nTPM
Adipose tissue	5.6 nTPM
Endometrium	4.1 nTPM
Kidney	2.3 nTPM
PBMC	0.0 nTPM

Paneth cells	13.5 nTPM
Rectum	19.3 nTPM
Small intestine	11.3 nTPM
Colon	9.9 nTPM

Plasma cells	14.3 nTPM
Stomach	19.0 nTPM
Bone marrow	18.2 nTPM
Spleen	14.1 nTPM
Esophagus	12.3 nTPM
Adipose tissue	7.8 nTPM

Respiratory ciliated cells	25.4 nTPM
Lung	29.1 nTPM
Bronchus	21.7 nTPM

Smooth muscle cells	7.7 nTPM
Heart muscle	12.4 nTPM
Esophagus	12.4 nTPM
Bronchus	9.5 nTPM
Pancreas	9.1 nTPM
Skeletal muscle	9.1 nTPM
Ovary	7.7 nTPM
Endometrium	7.6 nTPM
Adipose tissue	5.0 nTPM
Skin	4.9 nTPM
Breast	4.4 nTPM
Prostate	2.5 nTPM

T-cells	9.5 nTPM
Stomach	21.1 nTPM
Bone marrow	20.9 nTPM
Lymph node	16.1 nTPM
Liver	14.6 nTPM
Spleen	14.6 nTPM
Skeletal muscle	12.9 nTPM
Colon	11.4 nTPM
Breast	7.8 nTPM
PBMC	7.3 nTPM
Adipose tissue	6.3 nTPM
Lung	6.1 nTPM
Skin	5.5 nTPM
Endometrium	5.4 nTPM
Prostate	4.7 nTPM
Kidney	4.2 nTPM
Ovary	2.2 nTPM
Esophagus	0.0 nTPM

Basal squamous epithelial cells	25.6 nTPM
Esophagus	25.6 nTPM

Cholangiocytes	8.6 nTPM
Liver	8.6 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Cone photoreceptor cells	37.5 nTPM
Eye	37.5 nTPM

Undifferentiated cells	15.4 nTPM
Rectum	20.3 nTPM
Small intestine	16.2 nTPM
Colon	9.6 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