Single cell type - L3HYPDH - The Human Protein Atlas

L3HYPDH

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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.	L3HYPDH
Gene descriptionⁱ Full gene name according to HGNC.	Trans-L-3-hydroxyproline dehydratase
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.	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.	Adipocytes - 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 (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.	0.46
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.	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.	Low immune cell specificity
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 (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Low cell type specificity

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: Low cell type specificity

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: Low immune cell specificity
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

L3HYPDH is part of cluster 89 Adipocytes - Lipid metabolism with confidenceⁱ 1
142 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.
GPR135	G protein-coupled receptor 135	0.5498	2
TLN2	Talin 2	0.4551	89
ECM2	Extracellular matrix protein 2	0.4457	89
SETMAR	SET domain and mariner transposase fusion gene	0.4376	89
LHCGR	Luteinizing hormone/choriogonadotropin receptor	0.4350	89
WDPCP	WD repeat containing planar cell polarity effector	0.4299	89
ACACB	Acetyl-CoA carboxylase beta	0.4292	89
NUDT6	Nudix hydrolase 6	0.4262	89
AQP7	Aquaporin 7	0.4221	89
SLC15A5	Solute carrier family 15 member 5	0.4152	89
MTHFD1	Methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1	0.4066	89
TNS1	Tensin 1	0.4064	62
TRHDE	Thyrotropin releasing hormone degrading enzyme	0.4057	89
GHR	Growth hormone receptor	0.4000	89
NPR2	Natriuretic peptide receptor 2	0.3956	108

IMMUNE CELLS

L3HYPDH is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 1
757 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.
ENDOG	Endonuclease G	0.9524	33
SYNC	Syncoilin, intermediate filament protein	0.9524	33
RAD51AP1	RAD51 associated protein 1	0.9524	13
RABL2A	RAB, member of RAS oncogene family like 2A	0.9524	33
WASF1	WASP family member 1	0.9286	8
ZBED8	Zinc finger BED-type containing 8	0.9286	10
RPE	Ribulose-5-phosphate-3-epimerase	0.9286	10
NHLRC3	NHL repeat containing 3	0.9286	33
ZNF74	Zinc finger protein 74	0.9286	33
SOCS4	Suppressor of cytokine signaling 4	0.9286	33
FPGS	Folylpolyglutamate synthase	0.9286	8
DCTN6	Dynactin subunit 6	0.9286	8
PUM3	Pumilio RNA binding family member 3	0.9286	33
SPATA7	Spermatogenesis associated 7	0.9286	8
MBTPS2	Membrane bound transcription factor peptidase, site 2	0.9048	8

	Lacrimal acinar cells	Salivary acinar cells	Pancreatic acinar cells
Eye	6.3
Salivary gland		7.2
Pancreas			3.2
Mean exp	6.3	7.2	3.2

	Adipocytes
Heart muscle	43.2
Skeletal muscle	48.7
Adipose tissue	71.3
Mean exp	54.4

	Adrenal cortex cells	Adrenal medulla cells
Adrenal gland	20.4	0.0
Mean exp	20.4	0.0

	Alveolar cells type 1	Alveolar cells type 2	Transitional alveolar cells
Lung	21.8	4.8	4.7
Mean exp	21.8	4.8	4.7

	Esophageal apical cells
Esophagus	1.2
Mean exp	1.2

	B-cells
Brain	7.9
Eye	10.8
Lung	10.5
Salivary gland	11.7
Esophagus	7.3
Stomach	10.8
Liver	4.5
Kidney	7.1
Urinary bladder	4.0
Breast	16.1
Endometrium	3.0
Adipose tissue	17.8
Blood	13.1
Bone marrow	14.1
Lymph node	11.5
Spleen	15.8
Thymus	10.2
Mean exp	10.4

	Ocular epithelial cells	Mesothelial cells	Urothelial cells	Epicardial cells	Prostatic hillock cells
Eye	3.0
Urinary bladder			1.7
Prostate					6.4
Heart muscle				40.9
Adipose tissue		18.4
Thymus		13.2
Mean exp	3.0	15.8	1.7	40.9	6.4

	Respiratory basal cells	Esophageal basal cells	Salivary basal cells	Basal keratinocytes	Epididymal basal cells	Basal prostatic cells
Lung	5.6
Tongue				11.4
Salivary gland			5.7
Esophagus		12.2
Epididymis					5.3
Prostate						12.6
Skin				8.0
Mean exp	5.6	12.2	5.7	9.7	5.3	12.6

	Ependymal cells	Choroid plexus epithelial cells	Respiratory ciliated cells	Respiratory deuterosomal cells	Epididymal efferent duct ciliated cells	Fallopian tube ciliated cells	Endometrial ciliated cells
Brain	32.0	17.9
Lung			12.2	4.1
Epididymis					12.2
Fallopian tube						12.6
Endometrium							11.2
Mean exp	32.0	17.9	12.2	4.1	12.2	12.6	11.2

	Cdc	Pdcs
Lung		0.0
Breast	11.9	0.0
Endometrium		0.0
Adipose tissue	9.9
Skin	2.1
Blood		8.6
Lymph node	6.9
Mean exp	7.7	2.1

	Salivary duct cells	Cholangiocytes	Pancreatic duct cells	Renal collecting duct intercalated cells	Renal collecting duct principal cells	Renal connecting tubule cells	Epididymal efferent duct absorptive cells
Salivary gland	4.8
Liver		5.9
Pancreas			5.0
Kidney				7.4	8.1	12.5
Epididymis							7.8
Mean exp	4.8	5.9	5.0	7.4	8.1	12.5	7.8

	Vascular endothelial cells	Lymphatic endothelial cells
Brain	10.7
Eye	11.6	14.5
Pituitary gland	11.9
Lung	10.5	13.5
Tongue	11.2	13.2
Salivary gland	13.6	9.2
Esophagus	12.7	18.9
Stomach	9.5
Liver	11.3
Pancreas	13.5
Kidney	11.7	7.6
Urinary bladder	13.0	13.1
Testis	11.6	23.9
Epididymis	6.4
Prostate	13.5	19.5
Breast	15.4	16.6
Ovary	8.2	4.2
Fallopian tube	11.7	12.5
Endometrium	6.6	0.0
Placenta	14.3
Heart muscle	30.8
Skeletal muscle	5.6
Vasculature	13.5	12.9
Adipose tissue	11.4	9.8
Skin	7.4	5.7
Lymph node	12.9	8.0
Thymus	12.9	13.9
Spleen		10.4
Mean exp	12.0	12.0

	Enterocytes	Colonocytes
Small intestine	3.3
Colon		0.5
Rectum		4.1
Mean exp	3.3	2.3

	Neuroendocrine cells
Stomach	1.9
Small intestine	0.0
Colon	2.9
Rectum	1.8
Mean exp	1.7

	Erythrocyte progenitors	Erythrocytes
Blood		0.0
Bone marrow	5.5	0.0
Spleen		0.0
Mean exp	5.5	0.0

	Astrocytes	Bergmann glia	Müller glia	Pituicytes/fscs	Oligodendrocyte progenitor cells	Oligodendrocytes	Schwann cells	Microglia
Brain	18.7	14.7			18.8	22.0		16.6
Eye			5.0				0.0
Pituitary gland				15.4
Tongue							9.0
Urinary bladder							11.9
Vasculature							13.3
Mean exp	18.7	14.7	5.0	15.4	18.8	22.0	8.5	16.6

	Hepatocytes
Liver	25.0
Mean exp	25.0

	Fibro-adipogenic progenitors
Skeletal muscle	22.5
Adipose tissue	23.6
Mean exp	23.1

	Fibroblasts
Brain	34.5
Eye	18.3
Lung	21.3
Tongue	18.2
Salivary gland	21.1
Esophagus	17.5
Stomach	7.3
Pancreas	28.6
Kidney	17.8
Urinary bladder	18.4
Epididymis	4.5
Prostate	13.7
Breast	26.1
Fallopian tube	17.1
Placenta	18.1
Heart muscle	46.5
Vasculature	32.5
Skin	12.8
Lymph node	29.8
Thymus	24.3
Mean exp	21.4

	Foveolar cells	Mucous neck cells	Parietal cells	Gastric chief cells
Stomach	2.1	9.5	7.1	6.6
Mean exp	2.1	9.5	7.1	6.6

	Submucosal glandular cells	Prostatic glandular cells	Prostatic club cells	Endometrial glandular cells
Lung	5.5
Esophagus	5.1
Prostate		12.7	3.8
Endometrium				1.8
Mean exp	5.3	12.7	3.8	1.8

	Conjunctival goblet cells	Goblet cells
Eye	2.9
Small intestine		5.6
Colon		1.6
Rectum		7.8
Mean exp	2.9	5.0

	Innate lymphoid cells
Lung	0.0
Salivary gland	7.1
Urinary bladder	3.2
Breast	0.0
Fallopian tube	0.0
Endometrium	2.9
Lymph node	6.0
Thymus	6.4
Spleen	6.0
Mean exp	3.5

	Respiratory ionocytes	Salivary ionocytes
Lung	5.1
Salivary gland		4.0
Mean exp	5.1	4.0

	Breast hormone-responsive cells	Endometrial luminal cells
Breast	5.7
Endometrium		1.7
Mean exp	5.7	1.7

	Mast cells
Eye	5.5
Lung	6.1
Tongue	6.6
Salivary gland	16.2
Stomach	3.4
Pancreas	10.9
Urinary bladder	2.0
Epididymis	0.0
Fallopian tube	3.4
Vasculature	8.4
Adipose tissue	10.8
Lymph node	4.5
Mean exp	6.5

	Megakaryocyte progenitors	Megakaryocyte-erythroid progenitors	Megakaryocytes
Bone marrow	36.9	15.8	0.0
Mean exp	36.9	15.8	0.0

Acinar cells - 7.2 nCPM

Adipocytes - 54.4 nCPM

Adrenal endocrine cells - 20.4 nCPM

Alveolar cells - 21.8 nCPM

Apical squamous epithelial cells - 1.2 nCPM

B-cells - 10.4 nCPM

Barrier epithelial cells - 40.9 nCPM

Basal cells - 12.6 nCPM

Ciliated cells - 32.0 nCPM

Dendritic cells - 7.7 nCPM

Ductal cells - 12.5 nCPM

Endothelial cells - 12.0 nCPM

Enterocytes - 3.3 nCPM

Enteroendocrine cells - 1.7 nCPM

Erythrocytes - 5.5 nCPM

Fibro-adipogenic progenitors - 23.1 nCPM

Fibroblasts - 21.4 nCPM

Gastric glandular cells - 9.5 nCPM

Glandular cells - 12.7 nCPM

Glial cells - 22.0 nCPM

Goblet cells - 5.0 nCPM

Hepatocytes - 25.0 nCPM

Innate lymphoid cells - 3.5 nCPM

Ionocytes - 5.1 nCPM

Leydig cells - 28.5 nCPM

Luminal cells - 5.7 nCPM

Mast cells - 6.5 nCPM

Megakaryocytes - 36.9 nCPM

Mononuclear phagocytes - 11.2 nCPM

Mural cells - 14.8 nCPM

Myocytes - 41.4 nCPM

Neuronal cells - 27.1 nCPM

Neutrophils - 3.8 nCPM

Nk-cells - 4.2 nCPM

Oocytes - 9.2 nCPM

Pancreatic islet cells - 6.4 nCPM

Pigment cells - 8.5 nCPM

Pituitary endocrine cells - 31.0 nCPM

Plasma cells - 5.4 nCPM

Platelets - 2.8 nCPM

Proliferating cells - 4.6 nCPM

Renal nephron cells - 36.6 nCPM

Reproductive supporting cells - 23.0 nCPM

Secretory cells - 11.4 nCPM

Secretory gland support - 10.3 nCPM

Smooth muscle cells - 12.4 nCPM

Spermatogenic cell types - 20.3 nCPM

Stellate cells - 25.8 nCPM

Stem cells - 25.7 nCPM

Stromal cells - 24.6 nCPM

Suprabasal cells - 7.8 nCPM

T-cells - 9.3 nCPM

Trophoblast cells - 19.1 nCPM

	Monocyte progenitors	Monocytes	Macrophages	Kupffer cells	Hofbauer cells
Brain		9.3	17.8
Eye		5.0	6.8
Pituitary gland			8.0
Lung		7.0	10.0
Tongue		0.0	7.2
Salivary gland		3.4	9.6
Esophagus			4.0
Stomach		2.2	4.1
Liver		4.9	4.8	10.2
Pancreas		1.9	5.3
Kidney			9.9
Urinary bladder		3.6	6.5
Testis			8.5
Prostate		2.1	9.2
Breast		11.7	18.1
Ovary			0.0
Fallopian tube		3.5	5.3
Endometrium			3.1
Placenta					11.2
Heart muscle			17.4
Skeletal muscle			11.4
Vasculature		9.4	10.4
Adipose tissue			16.0
Skin			0.0
Blood		5.5
Bone marrow	6.4	6.5	9.2
Lymph node		4.5	10.1
Spleen		7.1	18.3
Thymus		5.4	9.5
Mean exp	6.4	5.2	8.9	10.2	11.2

	Pericytes	Vascular smooth muscle cells
Brain	17.8	8.8
Eye	20.8	5.8
Pituitary gland	14.2
Lung	9.2	14.3
Tongue	9.9	9.2
Salivary gland	17.4	8.6
Stomach	6.6	9.2
Pancreas	4.9
Kidney	15.6	13.9
Urinary bladder	7.5	9.1
Testis	4.2
Epididymis	12.3	3.1
Prostate	34.7	10.8
Breast	28.5	15.2
Ovary	11.9	8.8
Fallopian tube	16.0	7.7
Placenta	17.6
Heart muscle	22.4	28.4
Skeletal muscle	5.8	10.0
Vasculature	22.2	29.2
Adipose tissue	15.7	25.2
Skin	5.4	8.4
Thymus	20.4	10.8
Mean exp	14.8	12.4

	Cardiomyocytes	Myonuclei
Heart muscle	41.4
Skeletal muscle		17.7
Mean exp	41.4	17.7

	Brain excitatory neurons	Brain inhibitory neurons	Retinal amacrine cells	Retinal horizontal cells	Retinal ganglion cells	Retinal bipolar cells	Rod photoreceptor cells	Cone photoreceptor cells	Other brain neurons
Brain	27.1	19.5							17.9
Eye			2.8	10.0	7.7	2.1	3.4	2.1
Mean exp	27.1	19.5	2.8	10.0	7.7	2.1	3.4	2.1	17.9

	Neutrophil progenitors	Neutrophils
Eye		0.0
Lung		0.0
Salivary gland		1.4
Urinary bladder		0.0
Prostate		0.0
Vasculature		2.1
Blood	2.6	1.2
Bone marrow	6.0	0.7
Lymph node		1.9
Spleen	4.4	2.3
Thymus	2.3	1.3
Mean exp	3.8	1.0

	Nk-cells
Brain	3.7
Eye	3.5
Lung	5.5
Salivary gland	5.4
Stomach	0.0
Colon	0.0
Liver	3.4
Kidney	0.0
Urinary bladder	1.5
Prostate	3.1
Fallopian tube	3.6
Endometrium	1.6
Vasculature	6.7
Blood	7.2
Bone marrow	9.8
Lymph node	5.7
Thymus	8.6
Spleen	7.0
Mean exp	4.2

	Melanocytes	Retinal pigment epithelial cells
Eye	11.4	8.5
Skin	4.1
Mean exp	7.7	8.5

	Corticotrophs	Gonadotrophs	Lactotrophs	Somatotrophs	Thyrotrophs
Pituitary gland	13.2	17.6	24.3	31.0	16.5
Mean exp	13.2	17.6	24.3	31.0	16.5

	Plasma cells
Eye	6.4
Lung	3.0
Salivary gland	5.6
Stomach	13.9
Liver	3.4
Urinary bladder	5.7
Breast	0.0
Fallopian tube	3.8
Blood	6.7
Bone marrow	10.0
Lymph node	3.7
Spleen	4.0
Thymus	3.9
Mean exp	5.4

	Gastric progenitor cells	Enteric transient amplifying cells
Stomach	0.0
Small intestine		4.3
Colon		4.3
Rectum		5.2
Mean exp	0.0	4.6