Single cell type - WDR3 - The Human Protein Atlas

WDR3

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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.	WDR3
Gene descriptionⁱ Full gene name according to HGNC.	WD repeat domain 3
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.	2

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.	Late spermatids - 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 enhanced (Spermatocytes)
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.	0.39
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 (Spermatocytes)

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

WDR3 is part of cluster 11 Late spermatids - Unknown function with confidenceⁱ 1
430 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.
TSR1	TSR1 ribosome maturation factor	0.6526	39
MS4A5	Membrane spanning 4-domains A5	0.5432	11
TFAM	Transcription factor A, mitochondrial	0.5352	11
TEX35	Testis expressed 35	0.5346	11
SIRPD	Signal regulatory protein delta	0.5336	11
TWNK	Twinkle mtDNA helicase	0.5325	39
AKAP3	A-kinase anchoring protein 3	0.5286	11
GARIN2	Golgi associated RAB2 interactor family member 2	0.5268	11
TGS1	Trimethylguanosine synthase 1	0.5237	39
NOC3L	NOC3 like DNA replication regulator	0.5236	39
CIBAR1	CBY1 interacting BAR domain containing 1	0.5212	11
LTV1	LTV1 ribosome biogenesis factor	0.5207	39
MKRN2	Makorin ring finger protein 2	0.5198	11
ABCE1	ATP binding cassette subfamily E member 1	0.5186	39
ANKEF1	Ankyrin repeat and EF-hand domain containing 1	0.5126	11

IMMUNE CELLS

WDR3 is part of cluster 33 Non-specific - ATP binding with confidenceⁱ 0.98
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.
CSE1L	Chromosome segregation 1 like	1.0000	33
ZNF408	Zinc finger protein 408	0.9762	33
DDX3Y	DEAD-box helicase 3 Y-linked	0.9762	33
ZMYM2	Zinc finger MYM-type containing 2	0.9762	33
TPRG1	Tumor protein p63 regulated 1	0.9524	33
CCT4	Chaperonin containing TCP1 subunit 4	0.9524	33
IQCG	IQ motif containing G	0.9524	33
HSPA9	Heat shock protein family A (Hsp70) member 9	0.9524	33
ACOT13	Acyl-CoA thioesterase 13	0.9524	33
ZNF862	Zinc finger protein 862	0.9524	33
DOP1A	DOP1 leucine zipper like protein A	0.9524	33
POLR1B	RNA polymerase I subunit B	0.9286	33
EMC1	ER membrane protein complex subunit 1	0.9286	33
POMT1	Protein O-mannosyltransferase 1	0.9286	33
WDR36	WD repeat domain 36	0.9286	33

Adipocytes	10.6 nTPM
Breast	11.7 nTPM
Adipose tissue	9.5 nTPM

Alveolar cells type 1	21.9 nTPM
Lung	21.9 nTPM

Alveolar cells type 2	23.7 nTPM
Lung	23.7 nTPM

Astrocytes	5.6 nTPM
Brain	5.6 nTPM

B-cells	11.5 nTPM
Salivary gland	23.0 nTPM
Bone marrow	16.4 nTPM
Lymph node	15.8 nTPM
Kidney	15.6 nTPM
PBMC	15.4 nTPM
Spleen	14.8 nTPM
Thymus	11.0 nTPM
Skin	10.2 nTPM
Stomach	10.1 nTPM
Esophagus	5.9 nTPM
Adipose tissue	5.8 nTPM
Lung	5.4 nTPM
Liver	0.0 nTPM

Ciliated cells	9.6 nTPM
Fallopian tube	10.8 nTPM
Lung	10.4 nTPM
Endometrium	10.1 nTPM
Bronchus	7.0 nTPM

Club cells	8.2 nTPM
Bronchus	10.2 nTPM
Lung	8.0 nTPM
Prostate	6.3 nTPM

Endothelial cells	14.3 nTPM
Fallopian tube	32.8 nTPM
Lung	18.4 nTPM
Heart muscle	17.4 nTPM
Vascular	16.9 nTPM
Endometrium	16.1 nTPM
Pancreas	15.5 nTPM
Esophagus	14.7 nTPM
Skeletal muscle	14.3 nTPM
Salivary gland	14.3 nTPM
Thymus	14.3 nTPM
Testis	13.1 nTPM
Prostate	12.3 nTPM
Tongue	11.3 nTPM
Skin	11.1 nTPM
Placenta	9.7 nTPM
Ovary	9.4 nTPM
Breast	8.8 nTPM
Liver	7.6 nTPM

Enteroendocrine cells	6.8 nTPM
Colon	13.7 nTPM
Rectum	6.7 nTPM
Small intestine	0.0 nTPM

Fibroblasts	14.0 nTPM
Heart muscle	35.0 nTPM
Lung	20.4 nTPM
Fallopian tube	18.2 nTPM
Pancreas	17.0 nTPM
Salivary gland	15.4 nTPM
Stomach	14.4 nTPM
Skeletal muscle	14.1 nTPM
Thymus	12.9 nTPM
Vascular	12.6 nTPM
Liver	11.9 nTPM
Breast	10.3 nTPM
Adipose tissue	9.6 nTPM
Skin	8.7 nTPM
Esophagus	8.0 nTPM
Placenta	7.6 nTPM
Prostate	7.3 nTPM

Granulocytes	11.8 nTPM
Tongue	14.6 nTPM
Fallopian tube	10.8 nTPM
Lung	10.1 nTPM

Intestinal goblet cells	5.0 nTPM
Rectum	8.0 nTPM
Colon	4.7 nTPM
Small intestine	2.5 nTPM

Lymphatic endothelial cells	15.6 nTPM
Fallopian tube	20.3 nTPM
Ovary	10.9 nTPM

Macrophages	7.9 nTPM
Prostate	13.8 nTPM
Testis	13.0 nTPM
Bone marrow	12.2 nTPM
Thymus	11.7 nTPM
Salivary gland	10.9 nTPM
Tongue	9.3 nTPM
Endometrium	9.2 nTPM
Kidney	8.9 nTPM
Lung	8.4 nTPM
Breast	7.7 nTPM
Vascular	7.5 nTPM
Skeletal muscle	7.3 nTPM
Fallopian tube	6.7 nTPM
Esophagus	5.1 nTPM
Spleen	5.0 nTPM
Pancreas	4.1 nTPM
Adipose tissue	3.9 nTPM
Skin	3.3 nTPM
Stomach	2.6 nTPM

Paneth cells	6.3 nTPM
Rectum	8.5 nTPM
Small intestine	6.9 nTPM
Colon	3.6 nTPM

Basal keratinocytes	21.6 nTPM
Skin	23.5 nTPM
Tongue	19.7 nTPM

Basal prostatic cells	11.6 nTPM
Prostate	11.6 nTPM

Basal squamous epithelial cells	17.1 nTPM
Esophagus	17.1 nTPM

Cholangiocytes	5.7 nTPM
Liver	5.7 nTPM

Plasma cells	13.5 nTPM
Thymus	21.7 nTPM
Esophagus	20.8 nTPM
Fallopian tube	12.9 nTPM
Bone marrow	12.1 nTPM
Spleen	12.0 nTPM
Stomach	10.5 nTPM
Liver	9.5 nTPM
Salivary gland	8.5 nTPM

Schwann cells	6.3 nTPM
Vascular	11.5 nTPM
Adipose tissue	7.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	6.6 nTPM
Salivary gland	8.9 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	12.1 nTPM
Salivary gland	15.5 nTPM
Skeletal muscle	14.1 nTPM
Lung	14.1 nTPM
Endometrium	14.0 nTPM
Prostate	14.0 nTPM
Esophagus	13.2 nTPM
Skin	12.6 nTPM
Vascular	11.9 nTPM
Thymus	11.8 nTPM
Ovary	11.4 nTPM
Breast	11.2 nTPM
Tongue	10.5 nTPM
Fallopian tube	10.3 nTPM
Placenta	9.9 nTPM
Adipose tissue	9.8 nTPM
Liver	9.3 nTPM

Suprabasal keratinocytes	19.6 nTPM
Skin	22.4 nTPM
Tongue	16.8 nTPM

T-cells	11.4 nTPM
PBMC	18.4 nTPM
Esophagus	17.0 nTPM
Salivary gland	16.2 nTPM
Lymph node	15.4 nTPM
Bone marrow	15.1 nTPM
Lung	13.1 nTPM
Thymus	13.0 nTPM
Prostate	12.9 nTPM
Fallopian tube	12.6 nTPM
Stomach	11.5 nTPM
Breast	11.1 nTPM
Kidney	10.6 nTPM
Endometrium	10.1 nTPM
Spleen	9.7 nTPM
Tongue	9.7 nTPM
Vascular	9.2 nTPM
Skeletal muscle	8.7 nTPM
Adipose tissue	8.0 nTPM
Colon	6.8 nTPM
Liver	6.2 nTPM
Skin	3.5 nTPM

Undifferentiated cells	13.4 nTPM
Colon	18.8 nTPM
Rectum	12.3 nTPM
Small intestine	9.1 nTPM

Amygdala excitatory	23.5 nTPM
Hippocampus	27.8 nTPM
Thalamus	25.4 nTPM
Amygdala	24.5 nTPM
Cerebral cortex	23.5 nTPM
Basal ganglia	21.3 nTPM
Hypothalamus	18.7 nTPM

Astrocyte	10.7 nTPM
Hypothalamus	14.1 nTPM
Amygdala	12.7 nTPM
Thalamus	12.5 nTPM
Midbrain	11.6 nTPM
Basal ganglia	11.1 nTPM
Cerebral cortex	10.8 nTPM
Pons	10.6 nTPM
Medulla oblongata	10.1 nTPM
Hippocampus	9.5 nTPM
Cerebellum	8.5 nTPM
Spinal cord	6.7 nTPM

Bergmann glia	12.4 nTPM
Pons	12.9 nTPM
Medulla oblongata	12.8 nTPM
Cerebellum	11.6 nTPM

Central nervous system macrophage	17.7 nTPM
Amygdala	19.9 nTPM
Basal ganglia	19.4 nTPM
Hypothalamus	19.3 nTPM
Pons	18.1 nTPM
Thalamus	18.1 nTPM
Hippocampus	18.0 nTPM
Midbrain	17.9 nTPM
Cerebellum	17.5 nTPM
Medulla oblongata	16.9 nTPM
Spinal cord	15.0 nTPM
Cerebral cortex	14.8 nTPM

Cerebellar inhibitory	18.6 nTPM
Spinal cord	22.0 nTPM
Medulla oblongata	21.5 nTPM
Pons	18.4 nTPM
Cerebellum	17.2 nTPM
Midbrain	14.0 nTPM

Cge interneuron	19.0 nTPM
Thalamus	22.4 nTPM
Midbrain	19.2 nTPM
Amygdala	19.1 nTPM
Basal ganglia	19.0 nTPM
Hippocampus	18.7 nTPM
Cerebral cortex	18.6 nTPM
Hypothalamus	16.2 nTPM

Choroid plexus epithelial cell	46.5 nTPM
Thalamus	65.8 nTPM
Basal ganglia	42.5 nTPM
Hippocampus	41.6 nTPM
Medulla oblongata	36.1 nTPM

Committed oligodendrocyte precursor	17.6 nTPM
Medulla oblongata	25.8 nTPM
Amygdala	25.4 nTPM
Cerebral cortex	21.5 nTPM
Pons	17.7 nTPM
Hippocampus	17.6 nTPM
Midbrain	17.6 nTPM
Cerebellum	17.4 nTPM
Thalamus	14.4 nTPM
Hypothalamus	14.3 nTPM
Basal ganglia	11.0 nTPM
Spinal cord	11.0 nTPM

Deep-layer corticothalamic and 6b	18.4 nTPM
Hippocampus	20.3 nTPM
Basal ganglia	18.7 nTPM
Amygdala	18.6 nTPM
Cerebral cortex	18.6 nTPM
Midbrain	17.8 nTPM
Hypothalamus	16.5 nTPM

Deep-layer intratelencephalic	18.0 nTPM
Hippocampus	20.0 nTPM
Amygdala	19.2 nTPM
Basal ganglia	18.4 nTPM
Cerebral cortex	17.6 nTPM
Hypothalamus	14.8 nTPM

Deep-layer near-projecting	20.7 nTPM
Basal ganglia	23.4 nTPM
Cerebral cortex	22.6 nTPM
Amygdala	20.2 nTPM
Hippocampus	20.2 nTPM
Hypothalamus	17.3 nTPM

Eccentric medium spiny neuron	24.0 nTPM
Amygdala	26.1 nTPM
Hypothalamus	25.3 nTPM
Thalamus	24.9 nTPM
Cerebral cortex	23.5 nTPM
Basal ganglia	23.3 nTPM
Hippocampus	20.7 nTPM

Endothelial cell	14.6 nTPM
Spinal cord	20.7 nTPM
Hippocampus	20.2 nTPM
Cerebral cortex	19.2 nTPM
Medulla oblongata	17.4 nTPM
Amygdala	15.6 nTPM
Thalamus	14.1 nTPM
Basal ganglia	13.0 nTPM
Pons	12.5 nTPM
Hypothalamus	12.4 nTPM
Cerebellum	10.1 nTPM
Midbrain	5.7 nTPM