Single cell type - HDAC4 - 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.	HDAC4
Gene descriptionⁱ Full gene name according to HGNC.	Histone deacetylase 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes FDA approved drug targets 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.	6

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	Neurons & Oligodendrocytes - Neuronal signaling (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	Group enriched (Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor cells, Inhibitory neurons, Early spermatids, Astrocytes, Late spermatids, Microglial 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 (neutrophil, basophil)
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 (JURKAT, MOLT-4)
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: Group enriched (Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor cells, Inhibitory neurons, Early spermatids, Astrocytes, Late spermatids, Microglial 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

HDAC4 is part of cluster 21 Neurons & Oligodendrocytes - Neuronal signaling with confidenceⁱ 1
589 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
TECTA	Tectorin alpha	0.7421	21
DPY19L1	Dpy-19 like C-mannosyltransferase 1	0.6952	29
OR1F1	Olfactory receptor family 1 subfamily F member 1	0.6261	8
KIAA0319	KIAA0319	0.5969	21
NPIPB4	Nuclear pore complex interacting protein family member B4	0.5861	29
SLC36A1	Solute carrier family 36 member 1	0.5813	21
OR51B5	Olfactory receptor family 51 subfamily B member 5	0.5568	21
ARHGAP22	Rho GTPase activating protein 22	0.5560	42
FOXP2	Forkhead box P2	0.5475	21
RGS21	Regulator of G protein signaling 21	0.5450	29
DOCK4	Dedicator of cytokinesis 4	0.5445	21
ELAVL4	ELAV like RNA binding protein 4	0.5424	21
PSD3	Pleckstrin and Sec7 domain containing 3	0.5423	29
ERCC8	ERCC excision repair 8, CSA ubiquitin ligase complex subunit	0.5389	29
KCNMB4	Potassium calcium-activated channel subfamily M regulatory beta subunit 4	0.5373	21

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	8.6 nTPM
Adipose tissue	9.9 nTPM
Breast	7.4 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	7.4 nTPM
Lung	7.4 nTPM

B-cells	5.2 nTPM
Colon	9.6 nTPM
Adipose tissue	7.5 nTPM
Bone marrow	7.4 nTPM
Stomach	5.9 nTPM
Spleen	5.5 nTPM
Kidney	4.8 nTPM
Lymph node	4.8 nTPM
Liver	2.6 nTPM
Breast	2.6 nTPM
PBMC	1.4 nTPM

Basal keratinocytes	7.9 nTPM
Skin	7.9 nTPM

Dendritic cells	12.8 nTPM
Adipose tissue	20.8 nTPM
Breast	13.5 nTPM
PBMC	4.0 nTPM

Endothelial cells	7.1 nTPM
Skeletal muscle	12.9 nTPM
Endometrium	10.5 nTPM
Liver	10.1 nTPM
Esophagus	9.3 nTPM
Skin	9.0 nTPM
Heart muscle	8.7 nTPM
Ovary	8.0 nTPM
Breast	7.8 nTPM
Lung	6.2 nTPM
Prostate	6.1 nTPM
Placenta	4.6 nTPM
Testis	3.3 nTPM
Eye	2.4 nTPM
Pancreas	0.0 nTPM

Fibroblasts	14.0 nTPM
Skeletal muscle	35.4 nTPM
Adipose tissue	22.7 nTPM
Esophagus	19.5 nTPM
Breast	14.2 nTPM
Skin	13.6 nTPM
Lung	12.3 nTPM
Ovary	9.4 nTPM
Heart muscle	8.6 nTPM
Placenta	7.6 nTPM
Prostate	6.7 nTPM
Stomach	4.4 nTPM

Intestinal goblet cells	5.2 nTPM
Rectum	7.0 nTPM
Small intestine	5.8 nTPM
Colon	2.9 nTPM

Macrophages	10.3 nTPM
Stomach	23.5 nTPM
Skeletal muscle	21.1 nTPM
Bone marrow	16.3 nTPM
Spleen	14.5 nTPM
Adipose tissue	14.3 nTPM
Endometrium	12.3 nTPM
Esophagus	11.0 nTPM
Ovary	8.5 nTPM
Lung	7.5 nTPM
Breast	7.2 nTPM
Prostate	5.7 nTPM
Kidney	5.3 nTPM
Testis	4.6 nTPM
Pancreas	2.5 nTPM
PBMC	0.0 nTPM

Paneth cells	1.6 nTPM
Rectum	4.8 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	7.0 nTPM
Adipose tissue	24.5 nTPM
Spleen	5.3 nTPM
Stomach	3.6 nTPM
Bone marrow	1.7 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	2.6 nTPM
Bronchus	5.1 nTPM
Lung	0.0 nTPM

Smooth muscle cells	6.5 nTPM
Skeletal muscle	12.1 nTPM
Skin	11.8 nTPM
Endometrium	9.0 nTPM
Adipose tissue	7.5 nTPM
Ovary	6.6 nTPM
Prostate	6.2 nTPM
Breast	5.7 nTPM
Heart muscle	5.0 nTPM
Esophagus	4.6 nTPM
Bronchus	1.9 nTPM
Pancreas	1.5 nTPM

T-cells	12.2 nTPM
Skeletal muscle	24.7 nTPM
Adipose tissue	20.8 nTPM
Spleen	17.7 nTPM
Bone marrow	17.2 nTPM
Liver	13.6 nTPM
Lymph node	13.2 nTPM
PBMC	12.9 nTPM
Endometrium	12.8 nTPM
Colon	10.5 nTPM
Stomach	9.9 nTPM
Kidney	9.6 nTPM
Breast	9.6 nTPM
Prostate	9.5 nTPM
Ovary	8.9 nTPM
Skin	7.8 nTPM
Esophagus	6.6 nTPM
Lung	1.5 nTPM

Astrocytes	62.0 nTPM
Brain	62.0 nTPM

Cone photoreceptor cells	2.1 nTPM
Eye	2.1 nTPM

Endometrial stromal cells	15.1 nTPM
Endometrium	15.1 nTPM

Exocrine glandular cells	2.2 nTPM
Pancreas	2.2 nTPM

Undifferentiated cells	6.4 nTPM
Rectum	7.0 nTPM
Colon	6.6 nTPM
Small intestine	5.6 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