Single cell type - PDCD5 - The Human Protein Atlas

PDCD5

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Pathway

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.	PDCD5
Gene descriptionⁱ Full gene name according to HGNC.	Programmed cell death 5
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Plasma 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.	5

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.	Oocytes - Unknown function (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 enriched (Oocytes)
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.	0.45
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 enriched (Oocytes)

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

PDCD5 is part of cluster 44 Oocytes - Unknown function with confidenceⁱ 1
133 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.
C6orf52	Chromosome 6 open reading frame 52	0.8054	44
FOXR1	Forkhead box R1	0.7933	44
ENSG00000285471	Novel protein	0.7901	44
KPNA7	Karyopherin subunit alpha 7	0.7871	44
VRTN	Vertebrae development associated	0.7856	44
LHX8	LIM homeobox 8	0.7824	44
ZAR1	Zygote arrest 1	0.7795	44
H2BK1	H2B.K variant histone 1	0.7779	44
DPPA5	Developmental pluripotency associated 5	0.7774	44
SLC38A8	Solute carrier family 38 member 8	0.7753	44
ZP3	Zona pellucida glycoprotein 3	0.7749	44
OOSP4B	Oocyte secreted protein family member 4B	0.7745	44
TUBB8	Tubulin beta 8 class VIII	0.7728	44
KHDC3L	KH domain containing 3 like, subcortical maternal complex member	0.7700	44
KRTAP10-3	Keratin associated protein 10-3	0.7698	44

IMMUNE CELLS

PDCD5 is part of cluster 12 Non-specific - Mitochondrial translation with confidenceⁱ 0.99
566 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.
EDC4	Enhancer of mRNA decapping 4	0.9762	12
CMAS	Cytidine monophosphate N-acetylneuraminic acid synthetase	0.9762	12
SDAD1	SDA1 domain containing 1	0.9524	33
COX10	Cytochrome c oxidase assembly factor heme A:farnesyltransferase COX10	0.9524	12
FAM221A	Family with sequence similarity 221 member A	0.9524	12
SKA2	Spindle and kinetochore associated complex subunit 2	0.9524	9
CSTF3	Cleavage stimulation factor subunit 3	0.9524	12
PYM1	PYM homolog 1, exon junction complex associated factor	0.9524	12
RTCA	RNA 3'-terminal phosphate cyclase	0.9524	33
PCNA	Proliferating cell nuclear antigen	0.9524	9
MTRR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	0.9524	12
PMPCB	Peptidase, mitochondrial processing subunit beta	0.9524	12
LONP2	Lon peptidase 2, peroxisomal	0.9524	12
RTP4	Receptor transporter protein 4	0.9286	33
MRPL10	Mitochondrial ribosomal protein L10	0.9286	9

Adipocytes	108.3 nTPM
Breast	131.0 nTPM
Adipose tissue	85.6 nTPM

Alveolar cells type 1	221.5 nTPM
Lung	221.5 nTPM

Alveolar cells type 2	192.5 nTPM
Lung	192.5 nTPM

Astrocytes	15.8 nTPM
Brain	15.8 nTPM

B-cells	54.0 nTPM
Skin	86.4 nTPM
Spleen	75.2 nTPM
Liver	72.5 nTPM
Salivary gland	64.2 nTPM
PBMC	58.5 nTPM
Lymph node	56.9 nTPM
Thymus	56.1 nTPM
Lung	53.7 nTPM
Adipose tissue	48.6 nTPM
Bone marrow	44.2 nTPM
Stomach	42.2 nTPM
Kidney	31.2 nTPM
Esophagus	11.8 nTPM

Basal squamous epithelial cells	112.6 nTPM
Esophagus	112.6 nTPM

Ciliated cells	98.6 nTPM
Fallopian tube	128.7 nTPM
Endometrium	92.6 nTPM
Lung	90.7 nTPM
Bronchus	82.4 nTPM

Club cells	115.7 nTPM
Bronchus	132.6 nTPM
Lung	122.1 nTPM
Prostate	92.6 nTPM

Dendritic cells	42.2 nTPM
PBMC	57.6 nTPM
Adipose tissue	26.8 nTPM

Endothelial cells	125.6 nTPM
Lung	198.2 nTPM
Fallopian tube	196.9 nTPM
Pancreas	181.0 nTPM
Placenta	155.5 nTPM
Heart muscle	150.9 nTPM
Tongue	145.5 nTPM
Testis	139.8 nTPM
Thymus	139.3 nTPM
Breast	129.2 nTPM
Skin	111.3 nTPM
Skeletal muscle	110.0 nTPM
Ovary	103.3 nTPM
Endometrium	99.6 nTPM
Esophagus	87.5 nTPM
Liver	85.7 nTPM
Vascular	84.5 nTPM
Salivary gland	75.9 nTPM
Prostate	66.0 nTPM

Enteroendocrine cells	89.9 nTPM
Colon	123.6 nTPM
Small intestine	82.4 nTPM
Rectum	63.7 nTPM

Fibroblasts	151.4 nTPM
Pancreas	331.1 nTPM
Heart muscle	330.8 nTPM
Lung	229.5 nTPM
Fallopian tube	169.4 nTPM
Thymus	155.8 nTPM
Vascular	134.9 nTPM
Adipose tissue	133.8 nTPM
Skeletal muscle	132.4 nTPM
Breast	122.9 nTPM
Skin	121.3 nTPM
Placenta	111.8 nTPM
Salivary gland	97.4 nTPM
Prostate	94.4 nTPM
Esophagus	91.7 nTPM
Stomach	89.3 nTPM
Liver	75.9 nTPM

Granulocytes	63.7 nTPM
Fallopian tube	72.3 nTPM
Lung	65.5 nTPM
Tongue	53.4 nTPM

Intestinal goblet cells	86.2 nTPM
Colon	108.5 nTPM
Rectum	107.5 nTPM
Small intestine	42.7 nTPM

Lymphatic endothelial cells	143.8 nTPM
Ovary	158.2 nTPM
Fallopian tube	129.3 nTPM

Bipolar cells	41.0 nTPM
Eye	41.0 nTPM

Cholangiocytes	108.7 nTPM
Liver	108.7 nTPM

Collecting duct cells	79.7 nTPM
Kidney	79.7 nTPM

Cytotrophoblasts	210.2 nTPM
Placenta	210.2 nTPM

Macrophages	66.5 nTPM
Pancreas	137.7 nTPM
Testis	93.0 nTPM
Lung	92.9 nTPM
Breast	92.6 nTPM
Kidney	90.3 nTPM
Endometrium	84.3 nTPM
Thymus	74.5 nTPM
Tongue	71.1 nTPM
Prostate	69.7 nTPM
Fallopian tube	65.8 nTPM
Skeletal muscle	58.5 nTPM
Esophagus	50.1 nTPM
Skin	47.9 nTPM
Adipose tissue	46.0 nTPM
Stomach	43.7 nTPM
Bone marrow	42.6 nTPM
Vascular	42.0 nTPM
Salivary gland	38.9 nTPM
Spleen	21.1 nTPM

Paneth cells	97.1 nTPM
Rectum	132.8 nTPM
Small intestine	89.8 nTPM
Colon	68.8 nTPM

Plasma cells	159.5 nTPM
Thymus	232.2 nTPM
Liver	219.3 nTPM
Spleen	205.9 nTPM
Fallopian tube	154.1 nTPM
Bone marrow	149.5 nTPM
Salivary gland	112.8 nTPM
Stomach	103.0 nTPM
Esophagus	98.8 nTPM

Schwann cells	72.0 nTPM
Vascular	93.5 nTPM
Adipose tissue	74.6 nTPM
Esophagus	47.9 nTPM

Serous glandular cells	87.3 nTPM
Salivary gland	90.7 nTPM
Tongue	84.0 nTPM

Smooth muscle cells	137.6 nTPM
Placenta	238.6 nTPM
Fallopian tube	199.8 nTPM
Thymus	176.8 nTPM
Vascular	156.9 nTPM
Ovary	153.6 nTPM
Prostate	147.2 nTPM
Breast	143.9 nTPM
Skin	121.9 nTPM
Esophagus	121.3 nTPM
Skeletal muscle	119.5 nTPM
Lung	116.4 nTPM
Endometrium	115.2 nTPM
Liver	109.5 nTPM
Adipose tissue	96.4 nTPM
Salivary gland	94.3 nTPM
Tongue	90.7 nTPM

Suprabasal keratinocytes	208.6 nTPM
Tongue	301.9 nTPM
Skin	115.3 nTPM

T-cells	73.5 nTPM
Breast	102.2 nTPM
Fallopian tube	100.3 nTPM
Endometrium	95.8 nTPM
Kidney	87.8 nTPM
Prostate	83.9 nTPM
Skeletal muscle	83.6 nTPM
PBMC	81.1 nTPM
Liver	80.6 nTPM
Skin	78.9 nTPM
Tongue	76.0 nTPM
Lung	75.8 nTPM
Thymus	75.7 nTPM
Lymph node	65.7 nTPM
Spleen	65.6 nTPM
Adipose tissue	62.4 nTPM
Esophagus	60.8 nTPM
Stomach	57.6 nTPM
Bone marrow	55.6 nTPM
Salivary gland	55.5 nTPM
Vascular	53.5 nTPM
Colon	45.8 nTPM

Undifferentiated cells	169.8 nTPM
Colon	202.6 nTPM
Rectum	161.3 nTPM
Small intestine	145.6 nTPM

Amygdala excitatory	32.4 nTPM
Cerebral cortex	39.0 nTPM
Hippocampus	36.5 nTPM
Thalamus	36.3 nTPM
Basal ganglia	32.2 nTPM
Amygdala	29.2 nTPM
Hypothalamus	21.2 nTPM

Astrocyte	38.0 nTPM
Pons	44.8 nTPM
Midbrain	42.1 nTPM
Medulla oblongata	41.9 nTPM
Basal ganglia	41.5 nTPM
Hippocampus	41.2 nTPM
Cerebral cortex	39.2 nTPM
Thalamus	38.6 nTPM
Spinal cord	37.9 nTPM
Cerebellum	34.7 nTPM
Amygdala	29.8 nTPM
Hypothalamus	26.2 nTPM

Bergmann glia	43.7 nTPM
Pons	51.8 nTPM
Medulla oblongata	42.6 nTPM
Cerebellum	36.6 nTPM

Central nervous system macrophage	25.3 nTPM
Medulla oblongata	30.6 nTPM
Spinal cord	28.3 nTPM
Thalamus	28.2 nTPM
Cerebral cortex	26.8 nTPM
Pons	26.7 nTPM
Midbrain	26.3 nTPM
Basal ganglia	26.0 nTPM
Hippocampus	22.6 nTPM
Cerebellum	22.4 nTPM
Hypothalamus	21.6 nTPM
Amygdala	18.9 nTPM

Cerebellar inhibitory	45.0 nTPM
Pons	54.6 nTPM
Medulla oblongata	51.2 nTPM
Cerebellum	41.1 nTPM
Midbrain	39.5 nTPM
Spinal cord	38.5 nTPM

Cge interneuron	57.5 nTPM
Thalamus	80.9 nTPM
Midbrain	76.3 nTPM
Hippocampus	57.9 nTPM
Basal ganglia	56.1 nTPM
Cerebral cortex	50.2 nTPM
Amygdala	50.0 nTPM
Hypothalamus	31.1 nTPM

Choroid plexus epithelial cell	24.6 nTPM
Thalamus	32.9 nTPM
Hippocampus	30.5 nTPM
Medulla oblongata	23.8 nTPM
Basal ganglia	11.2 nTPM

Committed oligodendrocyte precursor	32.6 nTPM
Spinal cord	51.5 nTPM
Pons	44.3 nTPM
Thalamus	38.3 nTPM
Cerebellum	38.1 nTPM
Midbrain	32.8 nTPM
Hippocampus	30.5 nTPM
Basal ganglia	30.1 nTPM
Medulla oblongata	28.4 nTPM
Cerebral cortex	24.1 nTPM
Hypothalamus	21.8 nTPM
Amygdala	19.2 nTPM

Deep-layer corticothalamic and 6b	39.5 nTPM
Midbrain	56.6 nTPM
Basal ganglia	45.7 nTPM
Hippocampus	40.3 nTPM
Amygdala	37.6 nTPM
Cerebral cortex	36.7 nTPM
Hypothalamus	19.8 nTPM

Deep-layer intratelencephalic	37.0 nTPM
Basal ganglia	49.2 nTPM
Cerebral cortex	40.9 nTPM
Hippocampus	40.4 nTPM
Amygdala	34.2 nTPM
Hypothalamus	20.3 nTPM

Deep-layer near-projecting	58.4 nTPM
Hippocampus	83.9 nTPM
Cerebral cortex	68.8 nTPM
Basal ganglia	63.1 nTPM
Amygdala	48.5 nTPM
Hypothalamus	27.6 nTPM