Single cell type - RAD51B - The Human Protein Atlas

RAD51B

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(8 genes):

... PALB2 | RAD51 | RAD51B | RAD51D | SWSAP1 ...

Field

Term

Cluster

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.	RAD51B
Gene descriptionⁱ Full gene name according to HGNC.	RAD51 paralog B
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes 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.	8

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.	Oligodendrocyte precursor - 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.	Group enriched (Oligodendrocytes, Microglial cells, Oligodendrocyte precursor cells, Astrocytes)
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.	0.72
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 (Central nervous system macrophage)
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: Group enriched (Oligodendrocytes, Microglial cells, Oligodendrocyte precursor cells, Astrocytes)

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 (Central nervous system macrophage)

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

RAD51B is part of cluster 76 Oligodendrocyte precursor - Unknown function with confidenceⁱ 1
210 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.
ZC3H11A	Zinc finger CCCH-type containing 11A	0.6489	49
ENSG00000286098	Novel protein	0.6110	76
SGMS1	Sphingomyelin synthase 1	0.5973	76
SAP25	Sin3A associated protein 25	0.5970	47
BBS9	Bardet-Biedl syndrome 9	0.5962	51
DOCK4	Dedicator of cytokinesis 4	0.5960	34
ST6GALNAC3	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	0.5875	51
WWOX	WW domain containing oxidoreductase	0.5784	76
ZSWIM6	Zinc finger SWIM-type containing 6	0.5621	76
DOCK1	Dedicator of cytokinesis 1	0.5619	76
ZHX2	Zinc fingers and homeoboxes 2	0.5353	47
NCKAP5	NCK associated protein 5	0.5173	51
CHURC1-FNTB	CHURC1-FNTB readthrough	0.5106	76
PRORP	Protein only RNase P catalytic subunit	0.5105	7
TRIM62	Tripartite motif containing 62	0.5099	76

IMMUNE CELLS

RAD51B is part of cluster 32 Basophils - Transcription with confidenceⁱ 0.99
291 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.
TSPYL1	TSPY like 1	1.0000	32
LRCH3	Leucine rich repeats and calponin homology domain containing 3	1.0000	32
ANKRD42	Ankyrin repeat domain 42	0.9762	32
ENSG00000256646	Novel PSMA2 and C7orf25 readthrough	0.9762	42
POLR2J2	RNA polymerase II subunit J2	0.9762	32
INPP5B	Inositol polyphosphate-5-phosphatase B	0.9762	32
ZNF568	Zinc finger protein 568	0.9762	32
KMT5A	Lysine methyltransferase 5A	0.9762	32
KRCC1	Lysine rich coiled-coil 1	0.9762	32
CASP3	Caspase 3	0.9762	42
TTC19	Tetratricopeptide repeat domain 19	0.9762	42
PDHA1	Pyruvate dehydrogenase E1 subunit alpha 1	0.9762	42
TFAP2E	Transcription factor AP-2 epsilon	0.9762	32
CNOT4	CCR4-NOT transcription complex subunit 4	0.9762	32
AKAP11	A-kinase anchoring protein 11	0.9762	32

Adipocytes	4.6 nTPM
Adipose tissue	4.7 nTPM
Breast	4.5 nTPM

Alveolar cells type 1	0.8 nTPM
Lung	0.8 nTPM

Alveolar cells type 2	1.7 nTPM
Lung	1.7 nTPM

B-cells	11.5 nTPM
Bone marrow	26.9 nTPM
Lymph node	26.4 nTPM
Stomach	24.9 nTPM
Spleen	15.1 nTPM
Esophagus	11.8 nTPM
Lung	10.7 nTPM
Kidney	10.4 nTPM
Thymus	10.3 nTPM
Adipose tissue	6.2 nTPM
Salivary gland	5.8 nTPM
PBMC	1.5 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM

Basal keratinocytes	4.6 nTPM
Skin	6.0 nTPM
Tongue	3.2 nTPM

Ciliated cells	6.7 nTPM
Bronchus	11.1 nTPM
Lung	7.0 nTPM
Endometrium	5.2 nTPM
Fallopian tube	3.7 nTPM

Club cells	5.0 nTPM
Lung	6.9 nTPM
Bronchus	4.8 nTPM
Prostate	3.3 nTPM

Endothelial cells	4.3 nTPM
Placenta	14.2 nTPM
Esophagus	7.3 nTPM
Ovary	7.3 nTPM
Heart muscle	6.8 nTPM
Skeletal muscle	4.5 nTPM
Skin	4.0 nTPM
Vascular	3.9 nTPM
Endometrium	3.8 nTPM
Prostate	3.8 nTPM
Salivary gland	3.8 nTPM
Thymus	3.8 nTPM
Tongue	3.3 nTPM
Fallopian tube	3.2 nTPM
Testis	3.1 nTPM
Pancreas	2.6 nTPM
Breast	1.8 nTPM
Lung	1.2 nTPM
Liver	0.0 nTPM

Enteroendocrine cells	3.5 nTPM
Small intestine	6.9 nTPM
Colon	1.8 nTPM
Rectum	1.7 nTPM

Fibroblasts	3.5 nTPM
Thymus	6.9 nTPM
Esophagus	5.9 nTPM
Adipose tissue	5.8 nTPM
Breast	5.7 nTPM
Placenta	4.3 nTPM
Vascular	4.2 nTPM
Skeletal muscle	4.1 nTPM
Salivary gland	3.4 nTPM
Stomach	2.9 nTPM
Fallopian tube	2.9 nTPM
Pancreas	2.6 nTPM
Prostate	2.6 nTPM
Skin	2.3 nTPM
Heart muscle	2.0 nTPM
Lung	0.6 nTPM
Liver	0.0 nTPM

Granulocytes	5.0 nTPM
Fallopian tube	8.5 nTPM
Lung	6.6 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	4.8 nTPM
Rectum	7.3 nTPM
Colon	4.7 nTPM
Small intestine	2.4 nTPM

Lymphatic endothelial cells	7.3 nTPM
Ovary	10.9 nTPM
Fallopian tube	3.7 nTPM

Macrophages	4.8 nTPM
Bone marrow	11.1 nTPM
Breast	10.0 nTPM
Stomach	7.7 nTPM
Fallopian tube	5.4 nTPM
Lung	5.3 nTPM
Testis	5.0 nTPM
Skeletal muscle	4.8 nTPM
Prostate	4.8 nTPM
Skin	4.5 nTPM
Adipose tissue	4.4 nTPM
Tongue	4.4 nTPM
Spleen	4.0 nTPM
Thymus	3.9 nTPM
Salivary gland	3.5 nTPM
Endometrium	3.1 nTPM
Esophagus	2.6 nTPM
Vascular	2.6 nTPM
Pancreas	2.1 nTPM
Kidney	1.8 nTPM

Paneth cells	0.7 nTPM
Rectum	2.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Astrocytes	143.1 nTPM
Brain	143.1 nTPM

Bipolar cells	1.3 nTPM
Eye	1.3 nTPM

Cytotrophoblasts	5.6 nTPM
Placenta	5.6 nTPM

Plasma cells	6.4 nTPM
Esophagus	15.6 nTPM
Bone marrow	7.6 nTPM
Spleen	7.2 nTPM
Fallopian tube	6.4 nTPM
Stomach	4.6 nTPM
Thymus	4.4 nTPM
Salivary gland	3.1 nTPM
Liver	2.0 nTPM

Schwann cells	5.7 nTPM
Esophagus	12.0 nTPM
Adipose tissue	3.5 nTPM
Vascular	1.6 nTPM

Serous glandular cells	4.5 nTPM
Salivary gland	9.0 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	2.8 nTPM
Ovary	6.8 nTPM
Esophagus	4.8 nTPM
Skeletal muscle	4.2 nTPM
Breast	4.1 nTPM
Placenta	3.8 nTPM
Adipose tissue	3.8 nTPM
Endometrium	3.0 nTPM
Thymus	2.5 nTPM
Skin	2.3 nTPM
Salivary gland	2.2 nTPM
Fallopian tube	2.2 nTPM
Tongue	1.5 nTPM
Lung	1.2 nTPM
Prostate	1.2 nTPM
Vascular	1.1 nTPM
Liver	0.8 nTPM

T-cells	7.2 nTPM
Lymph node	22.0 nTPM
Spleen	16.5 nTPM
Bone marrow	15.0 nTPM
Stomach	12.1 nTPM
Salivary gland	7.8 nTPM
Breast	7.1 nTPM
Prostate	6.6 nTPM
Adipose tissue	6.1 nTPM
Fallopian tube	6.1 nTPM
Thymus	5.9 nTPM
Skin	5.3 nTPM
PBMC	4.9 nTPM
Skeletal muscle	4.9 nTPM
Esophagus	4.9 nTPM
Endometrium	4.6 nTPM
Liver	3.8 nTPM
Lung	3.7 nTPM
Tongue	3.6 nTPM
Kidney	3.5 nTPM
Colon	2.9 nTPM
Vascular	2.8 nTPM

Undifferentiated cells	2.3 nTPM
Colon	3.0 nTPM
Small intestine	2.1 nTPM
Rectum	1.7 nTPM

Amygdala excitatory	55.4 nTPM
Hypothalamus	78.7 nTPM
Amygdala	62.6 nTPM
Basal ganglia	59.1 nTPM
Thalamus	50.4 nTPM
Hippocampus	43.0 nTPM
Cerebral cortex	38.6 nTPM

Astrocyte	350.5 nTPM
Amygdala	523.5 nTPM
Hypothalamus	442.3 nTPM
Hippocampus	374.9 nTPM
Spinal cord	373.8 nTPM
Basal ganglia	369.6 nTPM
Cerebral cortex	330.0 nTPM
Medulla oblongata	324.2 nTPM
Midbrain	295.9 nTPM
Thalamus	286.8 nTPM
Pons	286.5 nTPM
Cerebellum	247.5 nTPM

Bergmann glia	344.7 nTPM
Medulla oblongata	370.8 nTPM
Cerebellum	341.1 nTPM
Pons	322.2 nTPM

Central nervous system macrophage	800.9 nTPM
Amygdala	1124.2 nTPM
Hypothalamus	1017.4 nTPM
Basal ganglia	833.2 nTPM
Hippocampus	817.2 nTPM
Midbrain	774.7 nTPM
Thalamus	764.6 nTPM
Pons	730.4 nTPM
Cerebral cortex	708.5 nTPM
Cerebellum	697.9 nTPM
Medulla oblongata	672.9 nTPM
Spinal cord	669.1 nTPM

Cerebellar inhibitory	43.2 nTPM
Spinal cord	74.2 nTPM
Midbrain	42.9 nTPM
Medulla oblongata	33.3 nTPM
Pons	33.1 nTPM
Cerebellum	32.4 nTPM

Cge interneuron	36.0 nTPM
Hypothalamus	45.9 nTPM
Amygdala	41.6 nTPM
Basal ganglia	34.7 nTPM
Thalamus	33.2 nTPM
Hippocampus	32.7 nTPM
Cerebral cortex	32.1 nTPM
Midbrain	31.6 nTPM

Choroid plexus epithelial cell	322.9 nTPM
Basal ganglia	421.9 nTPM
Thalamus	328.8 nTPM
Medulla oblongata	321.9 nTPM
Hippocampus	219.1 nTPM

Committed oligodendrocyte precursor	333.9 nTPM
Hypothalamus	478.0 nTPM
Amygdala	447.7 nTPM
Hippocampus	388.3 nTPM
Cerebellum	359.9 nTPM
Cerebral cortex	357.8 nTPM
Basal ganglia	332.9 nTPM
Thalamus	318.1 nTPM
Spinal cord	294.3 nTPM
Midbrain	285.6 nTPM
Pons	252.3 nTPM
Medulla oblongata	157.5 nTPM

Deep-layer corticothalamic and 6b	42.0 nTPM
Hypothalamus	55.9 nTPM
Hippocampus	47.5 nTPM
Amygdala	41.9 nTPM
Basal ganglia	41.7 nTPM
Cerebral cortex	37.2 nTPM
Midbrain	27.7 nTPM

Deep-layer intratelencephalic	59.3 nTPM
Amygdala	76.5 nTPM
Hypothalamus	65.5 nTPM
Hippocampus	55.6 nTPM
Basal ganglia	54.9 nTPM
Cerebral cortex	44.2 nTPM

Deep-layer near-projecting	64.7 nTPM
Hypothalamus	81.5 nTPM
Amygdala	74.1 nTPM
Basal ganglia	61.0 nTPM
Cerebral cortex	59.2 nTPM
Hippocampus	47.5 nTPM

Eccentric medium spiny neuron	39.5 nTPM
Hypothalamus	46.6 nTPM
Cerebral cortex	40.7 nTPM
Amygdala	40.0 nTPM
Basal ganglia	37.5 nTPM
Hippocampus	36.5 nTPM
Thalamus	36.0 nTPM

Endothelial cell	455.0 nTPM
Hypothalamus	746.9 nTPM
Basal ganglia	573.2 nTPM
Amygdala	495.2 nTPM
Thalamus	461.4 nTPM
Cerebellum	456.9 nTPM
Hippocampus	448.2 nTPM
Midbrain	417.7 nTPM
Cerebral cortex	410.4 nTPM
Spinal cord	334.8 nTPM
Medulla oblongata	331.3 nTPM
Pons	329.6 nTPM

Ependymal cell	758.8 nTPM
Basal ganglia	940.0 nTPM
Hypothalamus	902.2 nTPM
Amygdala	847.0 nTPM
Thalamus	793.3 nTPM
Hippocampus	734.0 nTPM
Spinal cord	726.4 nTPM
Pons	636.0 nTPM
Midbrain	631.7 nTPM
Medulla oblongata	618.4 nTPM