Single cell type - PDK4 - The Human Protein Atlas

PDK4

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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.	PDK4
Gene descriptionⁱ Full gene name according to HGNC.	Pyruvate dehydrogenase kinase 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic 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.	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.	Basal prostatic cells - Lipid metabolism (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.	Cell type enhanced (Basal prostatic cells, Skeletal myocytes, Cardiomyocytes, Adipocytes)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.56
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Choroid plexus epithelial cell, Astrocyte)
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.	Group enriched (intermediate monocyte, non-classical monocyte, eosinophil, classical monocyte, myeloid DC)
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Basal prostatic cells, Skeletal myocytes, Cardiomyocytes, Adipocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Choroid plexus epithelial cell, Astrocyte)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Group enriched (intermediate monocyte, non-classical monocyte, eosinophil, classical monocyte, myeloid DC)
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

PDK4 is part of cluster 3 Basal prostatic cells - Lipid metabolism with confidenceⁱ 1
162 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
KCNJ5	Potassium inwardly rectifying channel subfamily J member 5	0.7492	3
CST4	Cystatin S	0.6813	3
DEFB131A	Defensin beta 131A	0.6796	3
SPINT3	Serine peptidase inhibitor, Kunitz type 3	0.6728	3
CYP4F8	Cytochrome P450 family 4 subfamily F member 8	0.6682	3
SEMG1	Semenogelin 1	0.6664	3
TMEM114	Transmembrane protein 114	0.6658	3
SPINK13	Serine peptidase inhibitor Kazal type 13	0.6655	3
SEMG2	Semenogelin 2	0.6654	3
PATE1	Prostate and testis expressed 1	0.6651	3
PATE4	Prostate and testis expressed 4	0.6597	3
EDDM3A	Epididymal protein 3A	0.6578	3
GRXCR1	Glutaredoxin and cysteine rich domain containing 1	0.6551	3
PIP	Prolactin induced protein	0.6517	3
PRPS2	Phosphoribosyl pyrophosphate synthetase 2	0.6498	3

IMMUNE CELLS

PDK4 is part of cluster 25 Non-specific - Unknown function with confidenceⁱ 0.89
355 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
UGGT2	UDP-glucose glycoprotein glucosyltransferase 2	1.0000	25
TBXAS1	Thromboxane A synthase 1	1.0000	25
S100Z	S100 calcium binding protein Z	1.0000	25
NSMF	NMDA receptor synaptonuclear signaling and neuronal migration factor	1.0000	25
SIGLEC11	Sialic acid binding Ig like lectin 11	1.0000	25
PAQR7	Progestin and adipoQ receptor family member 7	0.9762	25
LKAAEAR1	LKAAEAR motif containing 1	0.9762	25
LGALS9	Galectin 9	0.9762	25
GFRA2	GDNF family receptor alpha 2	0.9762	25
SNAPC3	Small nuclear RNA activating complex polypeptide 3	0.9762	25
AGPAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	0.9762	25
CPT2	Carnitine palmitoyltransferase 2	0.9762	25
SORT1	Sortilin 1	0.9762	25
SPATA6	Spermatogenesis associated 6	0.9762	25
UBAC1	UBA domain containing 1	0.9762	25

Adipocytes	641.5 nTPM
Adipose tissue	1125.4 nTPM
Breast	157.5 nTPM

Alveolar cells type 1	17.0 nTPM
Lung	17.0 nTPM

Alveolar cells type 2	15.2 nTPM
Lung	15.2 nTPM

Astrocytes	146.5 nTPM
Brain	146.5 nTPM

B-cells	9.3 nTPM
Thymus	24.5 nTPM
Salivary gland	18.4 nTPM
Adipose tissue	17.7 nTPM
Esophagus	17.7 nTPM
Kidney	15.6 nTPM
Skin	8.5 nTPM
PBMC	4.6 nTPM
Lymph node	4.3 nTPM
Bone marrow	2.8 nTPM
Lung	2.7 nTPM
Stomach	2.1 nTPM
Spleen	1.8 nTPM
Liver	0.0 nTPM

Ciliated cells	119.9 nTPM
Fallopian tube	248.1 nTPM
Endometrium	147.7 nTPM
Lung	57.0 nTPM
Bronchus	27.0 nTPM

Club cells	73.9 nTPM
Prostate	184.0 nTPM
Lung	25.5 nTPM
Bronchus	12.1 nTPM

Endothelial cells	186.2 nTPM
Prostate	478.3 nTPM
Vascular	357.2 nTPM
Salivary gland	299.7 nTPM
Liver	282.2 nTPM
Skeletal muscle	241.4 nTPM
Thymus	227.3 nTPM
Lung	222.9 nTPM
Esophagus	204.2 nTPM
Heart muscle	202.2 nTPM
Ovary	148.3 nTPM
Skin	139.2 nTPM
Tongue	134.1 nTPM
Fallopian tube	127.6 nTPM
Breast	122.1 nTPM
Testis	89.1 nTPM
Endometrium	46.6 nTPM
Placenta	29.5 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	284.0 nTPM
Small intestine	717.5 nTPM
Colon	105.9 nTPM
Rectum	28.5 nTPM

Fibroblasts	334.1 nTPM
Adipose tissue	1352.4 nTPM
Stomach	631.2 nTPM
Salivary gland	630.4 nTPM
Thymus	534.2 nTPM
Prostate	495.0 nTPM
Vascular	471.1 nTPM
Liver	271.6 nTPM
Esophagus	210.8 nTPM
Skeletal muscle	192.5 nTPM
Heart muscle	172.7 nTPM
Skin	103.8 nTPM
Fallopian tube	102.0 nTPM
Breast	88.1 nTPM
Lung	82.9 nTPM
Placenta	5.0 nTPM
Pancreas	2.5 nTPM

Granulocytes	7.4 nTPM
Fallopian tube	10.4 nTPM
Lung	7.1 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	62.2 nTPM
Colon	107.5 nTPM
Small intestine	50.6 nTPM
Rectum	28.5 nTPM

Lymphatic endothelial cells	56.1 nTPM
Ovary	60.0 nTPM
Fallopian tube	52.1 nTPM

Macrophages	295.5 nTPM
Adipose tissue	1559.9 nTPM
Vascular	1112.6 nTPM
Thymus	760.7 nTPM
Salivary gland	548.1 nTPM
Prostate	316.6 nTPM
Esophagus	188.8 nTPM
Bone marrow	170.3 nTPM
Tongue	168.0 nTPM
Skeletal muscle	159.5 nTPM
Testis	103.5 nTPM
Stomach	97.7 nTPM
Spleen	93.2 nTPM
Lung	75.6 nTPM
Fallopian tube	75.4 nTPM
Endometrium	50.4 nTPM
Skin	46.8 nTPM
Breast	42.1 nTPM
Kidney	38.9 nTPM
Pancreas	6.2 nTPM

Paneth cells	41.0 nTPM
Small intestine	58.7 nTPM
Colon	32.6 nTPM
Rectum	31.6 nTPM

Cholangiocytes	24.8 nTPM
Liver	24.8 nTPM

Collecting duct cells	338.4 nTPM
Kidney	338.4 nTPM

Cytotrophoblasts	5.7 nTPM
Placenta	5.7 nTPM

Distal enterocytes	70.7 nTPM
Colon	117.6 nTPM
Rectum	23.7 nTPM

Plasma cells	20.0 nTPM
Esophagus	67.6 nTPM
Salivary gland	41.2 nTPM
Thymus	19.4 nTPM
Liver	13.0 nTPM
Stomach	10.5 nTPM
Fallopian tube	8.0 nTPM
Spleen	0.2 nTPM
Bone marrow	0.0 nTPM

Schwann cells	409.5 nTPM
Vascular	647.7 nTPM
Esophagus	443.3 nTPM
Adipose tissue	137.4 nTPM

Serous glandular cells	396.7 nTPM
Salivary gland	700.7 nTPM
Tongue	92.8 nTPM

Smooth muscle cells	347.0 nTPM
Adipose tissue	1020.1 nTPM
Prostate	810.1 nTPM
Thymus	614.8 nTPM
Esophagus	539.4 nTPM
Vascular	433.1 nTPM
Salivary gland	414.0 nTPM
Lung	353.9 nTPM
Skin	318.2 nTPM
Fallopian tube	208.2 nTPM
Tongue	194.6 nTPM
Ovary	190.9 nTPM
Skeletal muscle	189.5 nTPM
Liver	144.3 nTPM
Breast	70.5 nTPM
Placenta	31.7 nTPM
Endometrium	19.4 nTPM

T-cells	22.0 nTPM
Prostate	340.2 nTPM
Vascular	31.0 nTPM
Endometrium	17.4 nTPM
Salivary gland	14.1 nTPM
Skeletal muscle	11.3 nTPM
Fallopian tube	8.2 nTPM
Skin	7.0 nTPM
Lung	6.0 nTPM
Esophagus	4.9 nTPM
Tongue	4.3 nTPM
Liver	4.0 nTPM
Kidney	3.5 nTPM
Breast	2.8 nTPM
Colon	1.9 nTPM
Adipose tissue	1.9 nTPM
Thymus	1.6 nTPM
Stomach	0.6 nTPM
Spleen	0.2 nTPM
PBMC	0.1 nTPM
Bone marrow	0.1 nTPM
Lymph node	0.0 nTPM

Undifferentiated cells	45.8 nTPM
Small intestine	64.7 nTPM
Colon	55.3 nTPM
Rectum	17.5 nTPM

Amygdala excitatory	0.3 nTPM
Amygdala	0.5 nTPM
Hypothalamus	0.5 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.2 nTPM
Thalamus	0.0 nTPM

Astrocyte	151.4 nTPM
Basal ganglia	580.3 nTPM
Midbrain	285.0 nTPM
Amygdala	141.9 nTPM
Cerebral cortex	138.2 nTPM
Thalamus	134.3 nTPM
Hippocampus	102.5 nTPM
Hypothalamus	84.7 nTPM
Pons	75.6 nTPM
Cerebellum	45.4 nTPM
Spinal cord	40.3 nTPM
Medulla oblongata	37.6 nTPM

Bergmann glia	36.1 nTPM
Cerebellum	41.6 nTPM
Pons	38.8 nTPM
Medulla oblongata	27.7 nTPM

Central nervous system macrophage	22.6 nTPM
Cerebral cortex	57.9 nTPM
Basal ganglia	46.6 nTPM
Hippocampus	27.1 nTPM
Amygdala	26.0 nTPM
Midbrain	24.8 nTPM
Thalamus	17.0 nTPM
Cerebellum	15.0 nTPM
Hypothalamus	14.5 nTPM
Medulla oblongata	8.6 nTPM
Pons	7.2 nTPM
Spinal cord	4.4 nTPM

Cerebellar inhibitory	0.2 nTPM
Medulla oblongata	0.4 nTPM
Pons	0.3 nTPM
Cerebellum	0.2 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	1.2 nTPM
Thalamus	2.5 nTPM
Cerebral cortex	1.5 nTPM
Midbrain	1.3 nTPM
Amygdala	1.0 nTPM
Hypothalamus	0.8 nTPM
Hippocampus	0.6 nTPM
Basal ganglia	0.5 nTPM

Choroid plexus epithelial cell	410.2 nTPM
Hippocampus	648.9 nTPM
Thalamus	394.6 nTPM
Medulla oblongata	332.2 nTPM
Basal ganglia	265.0 nTPM

Committed oligodendrocyte precursor	24.0 nTPM
Medulla oblongata	60.7 nTPM
Basal ganglia	44.9 nTPM
Thalamus	31.1 nTPM
Hypothalamus	28.7 nTPM
Amygdala	20.9 nTPM
Cerebral cortex	20.3 nTPM
Hippocampus	16.8 nTPM
Midbrain	15.1 nTPM
Cerebellum	11.1 nTPM
Pons	10.6 nTPM
Spinal cord	3.7 nTPM

Deep-layer corticothalamic and 6b	0.3 nTPM
Basal ganglia	0.5 nTPM
Cerebral cortex	0.4 nTPM
Amygdala	0.3 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.3 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.3 nTPM
Cerebral cortex	0.3 nTPM
Hippocampus	0.3 nTPM
Hypothalamus	0.1 nTPM

Deep-layer near-projecting	0.1 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.2 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.2 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM

Endothelial cell	83.9 nTPM
Basal ganglia	176.2 nTPM
Cerebral cortex	147.7 nTPM
Amygdala	90.5 nTPM
Midbrain	82.2 nTPM
Cerebellum	81.3 nTPM
Spinal cord	79.4 nTPM
Hypothalamus	70.7 nTPM
Medulla oblongata	62.6 nTPM
Pons	51.8 nTPM
Hippocampus	43.0 nTPM
Thalamus	37.8 nTPM

Ependymal cell	36.7 nTPM
Hypothalamus	133.0 nTPM
Basal ganglia	60.6 nTPM
Thalamus	36.4 nTPM
Amygdala	28.4 nTPM
Spinal cord	17.2 nTPM
Hippocampus	16.4 nTPM
Midbrain	14.6 nTPM
Medulla oblongata	13.8 nTPM
Pons	10.2 nTPM