Single cell type - PNKD - The Human Protein Atlas

PNKD

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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.	PNKD
Gene descriptionⁱ Full gene name according to HGNC.	PNKD metallo-beta-lactamase domain containing
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes 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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	10

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.	Non-specific - Basic cellular processes (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 (Distal tubular cells)
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.	0.28
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 (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 (Distal tubular cells)

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

PNKD is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 0.98
835 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.
TSTD1	Thiosulfate sulfurtransferase like domain containing 1	0.6352	5
COA3	Cytochrome c oxidase assembly factor 3	0.6093	39
NDUFB7	NADH:ubiquinone oxidoreductase subunit B7	0.5949	39
MRPS26	Mitochondrial ribosomal protein S26	0.5642	39
PRDX3	Peroxiredoxin 3	0.5497	39
CHCHD5	Coiled-coil-helix-coiled-coil-helix domain containing 5	0.5472	39
ATP5F1D	ATP synthase F1 subunit delta	0.5451	5
CHCHD1	Coiled-coil-helix-coiled-coil-helix domain containing 1	0.5417	39
COQ9	Coenzyme Q9	0.5304	39
POP5	POP5 homolog, ribonuclease P/MRP subunit	0.5292	39
TRAPPC6A	Trafficking protein particle complex subunit 6A	0.5228	56
DMAC1	Distal membrane arm assembly component 1	0.5213	39
ATP5MC3	ATP synthase membrane subunit c locus 3	0.5201	39
CHCHD10	Coiled-coil-helix-coiled-coil-helix domain containing 10	0.5158	39
MRPS35	Mitochondrial ribosomal protein S35	0.5151	39

IMMUNE CELLS

PNKD is part of cluster 25 Non-specific - Unknown function with confidenceⁱ 0.5
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.
ENSG00000258674	Novel protein	0.9762	36
CLN5	CLN5 intracellular trafficking protein	0.9762	25
COMMD5	COMM domain containing 5	0.9762	25
KCNK6	Potassium two pore domain channel subfamily K member 6	0.9524	36
TSC2	TSC complex subunit 2	0.9524	25
RBM42	RNA binding motif protein 42	0.9524	36
ZHX1-C8orf76	ZHX1-C8orf76 readthrough	0.9286	25
NSFL1C	NSFL1 cofactor	0.9286	22
COA3	Cytochrome c oxidase assembly factor 3	0.9286	42
LFNG	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0.9286	25
C1orf131	Chromosome 1 open reading frame 131	0.9286	22
HARS2	Histidyl-tRNA synthetase 2, mitochondrial	0.9286	25
PSMA2	Proteasome 20S subunit alpha 2	0.9048	36
TTC1	Tetratricopeptide repeat domain 1	0.9048	36
SUFU	SUFU negative regulator of hedgehog signaling	0.9048	36

Adipocytes	86.6 nTPM
Breast	109.6 nTPM
Adipose tissue	63.7 nTPM

Alveolar cells type 1	66.1 nTPM
Lung	66.1 nTPM

Alveolar cells type 2	150.0 nTPM
Lung	150.0 nTPM

Astrocytes	28.5 nTPM
Brain	28.5 nTPM

B-cells	54.9 nTPM
Kidney	88.4 nTPM
Lung	79.1 nTPM
PBMC	78.5 nTPM
Bone marrow	66.2 nTPM
Salivary gland	60.4 nTPM
Thymus	49.1 nTPM
Esophagus	47.2 nTPM
Spleen	46.7 nTPM
Liver	43.5 nTPM
Lymph node	42.7 nTPM
Skin	42.3 nTPM
Adipose tissue	35.8 nTPM
Stomach	33.3 nTPM

Ciliated cells	130.2 nTPM
Bronchus	153.6 nTPM
Endometrium	131.0 nTPM
Fallopian tube	125.4 nTPM
Lung	110.8 nTPM

Club cells	151.6 nTPM
Prostate	186.3 nTPM
Bronchus	170.9 nTPM
Lung	97.6 nTPM

Dendritic cells	34.3 nTPM
PBMC	46.8 nTPM
Adipose tissue	21.9 nTPM

Endothelial cells	73.3 nTPM
Breast	119.5 nTPM
Placenta	104.5 nTPM
Tongue	104.1 nTPM
Ovary	95.7 nTPM
Testis	90.7 nTPM
Liver	88.2 nTPM
Heart muscle	85.7 nTPM
Prostate	75.5 nTPM
Skeletal muscle	71.9 nTPM
Skin	69.4 nTPM
Fallopian tube	66.8 nTPM
Thymus	56.9 nTPM
Salivary gland	53.5 nTPM
Endometrium	53.3 nTPM
Esophagus	50.9 nTPM
Pancreas	46.5 nTPM
Vascular	45.6 nTPM
Lung	41.3 nTPM

Enteroendocrine cells	165.0 nTPM
Colon	230.4 nTPM
Rectum	137.5 nTPM
Small intestine	127.0 nTPM

Fibroblasts	89.0 nTPM
Placenta	160.7 nTPM
Heart muscle	142.9 nTPM
Prostate	114.2 nTPM
Skin	107.7 nTPM
Breast	101.0 nTPM
Adipose tissue	92.9 nTPM
Fallopian tube	91.8 nTPM
Liver	87.8 nTPM
Esophagus	84.6 nTPM
Pancreas	71.6 nTPM
Skeletal muscle	69.3 nTPM
Salivary gland	66.4 nTPM
Thymus	59.6 nTPM
Vascular	59.6 nTPM
Lung	58.7 nTPM
Stomach	54.8 nTPM

Granulocytes	46.3 nTPM
Lung	72.1 nTPM
Fallopian tube	47.3 nTPM
Tongue	19.4 nTPM

Intestinal goblet cells	161.0 nTPM
Colon	194.4 nTPM
Rectum	172.9 nTPM
Small intestine	115.6 nTPM

Lymphatic endothelial cells	72.8 nTPM
Ovary	76.4 nTPM
Fallopian tube	69.2 nTPM

Macrophages	65.3 nTPM
Kidney	100.0 nTPM
Spleen	94.2 nTPM
Stomach	84.9 nTPM
Fallopian tube	81.1 nTPM
Bone marrow	80.1 nTPM
Pancreas	76.1 nTPM
Thymus	75.6 nTPM
Esophagus	71.9 nTPM
Prostate	63.4 nTPM
Vascular	60.7 nTPM
Lung	59.7 nTPM
Tongue	59.6 nTPM
Endometrium	54.7 nTPM
Breast	53.2 nTPM
Salivary gland	52.9 nTPM
Skeletal muscle	51.6 nTPM
Testis	42.2 nTPM
Adipose tissue	39.7 nTPM
Skin	39.0 nTPM

Basal prostatic cells	158.3 nTPM
Prostate	158.3 nTPM

Basal respiratory cells	174.8 nTPM
Bronchus	174.8 nTPM

Basal squamous epithelial cells	93.5 nTPM
Esophagus	93.5 nTPM

Cholangiocytes	135.5 nTPM
Liver	135.5 nTPM

Paneth cells	133.2 nTPM
Colon	155.6 nTPM
Rectum	150.8 nTPM
Small intestine	93.3 nTPM

Plasma cells	80.1 nTPM
Spleen	99.6 nTPM
Bone marrow	90.6 nTPM
Thymus	90.3 nTPM
Liver	89.6 nTPM
Stomach	75.8 nTPM
Salivary gland	68.5 nTPM
Esophagus	67.6 nTPM
Fallopian tube	58.5 nTPM

Schwann cells	44.7 nTPM
Vascular	65.8 nTPM
Esophagus	47.9 nTPM
Adipose tissue	20.3 nTPM

Serous glandular cells	114.7 nTPM
Tongue	119.3 nTPM
Salivary gland	110.2 nTPM

Smooth muscle cells	98.4 nTPM
Placenta	154.7 nTPM
Ovary	145.3 nTPM
Fallopian tube	134.1 nTPM
Prostate	129.5 nTPM
Breast	126.2 nTPM
Esophagus	117.7 nTPM
Lung	87.0 nTPM
Liver	83.6 nTPM
Salivary gland	83.6 nTPM
Skin	81.2 nTPM
Tongue	78.7 nTPM
Vascular	75.1 nTPM
Adipose tissue	74.8 nTPM
Skeletal muscle	72.0 nTPM
Endometrium	70.9 nTPM
Thymus	59.5 nTPM

Suprabasal keratinocytes	94.4 nTPM
Tongue	133.4 nTPM
Skin	55.4 nTPM

T-cells	51.5 nTPM
Kidney	77.1 nTPM
Liver	76.1 nTPM
Prostate	75.1 nTPM
PBMC	64.7 nTPM
Esophagus	63.3 nTPM
Lung	61.1 nTPM
Breast	54.5 nTPM
Skin	54.3 nTPM
Endometrium	53.5 nTPM
Bone marrow	51.4 nTPM
Spleen	50.8 nTPM
Tongue	49.7 nTPM
Salivary gland	47.1 nTPM
Thymus	43.8 nTPM
Skeletal muscle	40.5 nTPM
Stomach	39.0 nTPM
Vascular	39.0 nTPM
Fallopian tube	38.2 nTPM
Colon	37.0 nTPM
Lymph node	36.4 nTPM
Adipose tissue	28.3 nTPM

Undifferentiated cells	163.7 nTPM
Colon	172.0 nTPM
Rectum	162.6 nTPM
Small intestine	156.6 nTPM

Amygdala excitatory	46.7 nTPM
Hypothalamus	53.0 nTPM
Amygdala	46.9 nTPM
Thalamus	46.7 nTPM
Hippocampus	46.2 nTPM
Cerebral cortex	44.8 nTPM
Basal ganglia	42.3 nTPM

Astrocyte	39.0 nTPM
Pons	47.1 nTPM
Cerebral cortex	45.4 nTPM
Thalamus	44.9 nTPM
Basal ganglia	44.8 nTPM
Cerebellum	44.3 nTPM
Midbrain	40.8 nTPM
Medulla oblongata	39.7 nTPM
Hippocampus	36.6 nTPM
Spinal cord	31.8 nTPM
Hypothalamus	27.9 nTPM
Amygdala	25.2 nTPM

Bergmann glia	47.8 nTPM
Medulla oblongata	70.3 nTPM
Cerebellum	42.8 nTPM
Pons	30.2 nTPM

Central nervous system macrophage	36.7 nTPM
Medulla oblongata	42.0 nTPM
Cerebral cortex	41.8 nTPM
Basal ganglia	39.0 nTPM
Thalamus	39.0 nTPM
Midbrain	38.1 nTPM
Pons	37.4 nTPM
Cerebellum	37.0 nTPM
Hippocampus	35.5 nTPM
Spinal cord	34.4 nTPM
Hypothalamus	31.7 nTPM
Amygdala	27.3 nTPM

Cerebellar inhibitory	68.0 nTPM
Pons	79.7 nTPM
Medulla oblongata	72.2 nTPM
Midbrain	66.3 nTPM
Spinal cord	63.2 nTPM
Cerebellum	58.4 nTPM

Cge interneuron	49.5 nTPM
Thalamus	66.3 nTPM
Midbrain	55.2 nTPM
Hippocampus	46.2 nTPM
Basal ganglia	45.2 nTPM
Cerebral cortex	45.1 nTPM
Amygdala	45.0 nTPM
Hypothalamus	43.2 nTPM

Choroid plexus epithelial cell	49.3 nTPM
Hippocampus	77.7 nTPM
Medulla oblongata	48.2 nTPM
Thalamus	41.1 nTPM
Basal ganglia	30.2 nTPM

Committed oligodendrocyte precursor	40.9 nTPM
Medulla oblongata	64.5 nTPM
Pons	50.5 nTPM
Midbrain	47.9 nTPM
Cerebellum	46.0 nTPM
Basal ganglia	42.7 nTPM
Spinal cord	40.5 nTPM
Cerebral cortex	39.3 nTPM
Thalamus	35.1 nTPM
Hippocampus	32.6 nTPM
Hypothalamus	28.0 nTPM
Amygdala	23.1 nTPM

Deep-layer corticothalamic and 6b	44.8 nTPM
Hippocampus	51.7 nTPM
Hypothalamus	49.4 nTPM
Cerebral cortex	45.8 nTPM
Basal ganglia	41.7 nTPM
Amygdala	40.3 nTPM
Midbrain	39.9 nTPM

Deep-layer intratelencephalic	48.8 nTPM
Hypothalamus	56.0 nTPM
Cerebral cortex	52.7 nTPM
Hippocampus	47.3 nTPM
Amygdala	44.2 nTPM
Basal ganglia	43.9 nTPM

Deep-layer near-projecting	57.9 nTPM
Hippocampus	62.4 nTPM
Cerebral cortex	61.9 nTPM
Hypothalamus	57.4 nTPM
Amygdala	56.4 nTPM
Basal ganglia	51.2 nTPM

Eccentric medium spiny neuron	38.7 nTPM
Thalamus	43.7 nTPM
Cerebral cortex	41.1 nTPM
Basal ganglia	40.6 nTPM
Amygdala	39.7 nTPM
Hypothalamus	35.3 nTPM
Hippocampus	31.9 nTPM