Single cell type - RAB7B - The Human Protein Atlas

RAB7B

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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.	RAB7B
Gene descriptionⁱ Full gene name according to HGNC.	RAB7B, member RAS oncogene family
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.	4

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.	Dendritic cells - Antigen presentation (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 (Langerhans cells, Schwann cells, Mesothelial cells, Hofbauer 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.	0.78
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 (Oligodendrocyte, Fibroblast, Committed oligodendrocyte precursor)
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.	Immune cell enriched (myeloid DC)
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 (Langerhans cells, Schwann cells, Mesothelial cells, Hofbauer 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: Cell type enhanced (Oligodendrocyte, Fibroblast, Committed oligodendrocyte precursor)

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: Immune cell enriched (myeloid DC)
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

RAB7B is part of cluster 28 Dendritic cells - Antigen presentation with confidenceⁱ 1
245 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.
CD1C	CD1c molecule	0.8835	28
CPVL	Carboxypeptidase vitellogenic like	0.8742	28
HLA-DPB1	Major histocompatibility complex, class II, DP beta 1	0.8724	28
GPR157	G protein-coupled receptor 157	0.8720	28
XCR1	X-C motif chemokine receptor 1	0.8578	28
CD1A	CD1a molecule	0.8571	28
HLA-DQA1	Major histocompatibility complex, class II, DQ alpha 1	0.8568	28
CLEC10A	C-type lectin domain containing 10A	0.8556	28
CST3	Cystatin C	0.8541	28
CLEC9A	C-type lectin domain containing 9A	0.8520	28
CD1E	CD1e molecule	0.8511	28
HLA-DPA1	Major histocompatibility complex, class II, DP alpha 1	0.8483	28
FCER1A	Fc epsilon receptor Ia	0.8465	28
HLA-DRA	Major histocompatibility complex, class II, DR alpha	0.8452	28
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1	0.8448	28

IMMUNE CELLS

RAB7B is part of cluster 2 Dendritic cells - Unknown function with confidenceⁱ 0.66
342 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.
OAF	Out at first homolog	0.9762	2
RAB13	RAB13, member RAS oncogene family	0.9762	2
DEPTOR	DEP domain containing MTOR interacting protein	0.9762	2
GRIP1	Glutamate receptor interacting protein 1	0.9762	2
CABP1	Calcium binding protein 1	0.9524	2
MRC1	Mannose receptor C-type 1	0.9524	2
CES1	Carboxylesterase 1	0.9524	2
LHFPL6	LHFPL tetraspan subfamily member 6	0.9524	2
FZD2	Frizzled class receptor 2	0.9524	2
ERICH5	Glutamate rich 5	0.9524	2
WDR49	WD repeat domain 49	0.9524	2
ENDOV	Endonuclease V	0.9524	2
COL8A2	Collagen type VIII alpha 2 chain	0.9524	2
CTTNBP2NL	CTTNBP2 N-terminal like	0.9524	2
EMP1	Epithelial membrane protein 1	0.9524	2

Adipocytes	0.4 nTPM
Breast	0.9 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	3.5 nTPM
Lung	3.5 nTPM

Alveolar cells type 2	3.0 nTPM
Lung	3.0 nTPM

Astrocytes	1.2 nTPM
Brain	1.2 nTPM

B-cells	9.8 nTPM
Skin	123.7 nTPM
Lung	1.3 nTPM
Thymus	1.1 nTPM
Spleen	0.6 nTPM
Lymph node	0.2 nTPM
Salivary gland	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Ciliated cells	1.1 nTPM
Bronchus	1.8 nTPM
Lung	1.1 nTPM
Endometrium	0.8 nTPM
Fallopian tube	0.8 nTPM

Club cells	4.4 nTPM
Lung	8.0 nTPM
Bronchus	4.0 nTPM
Prostate	1.0 nTPM

Endothelial cells	0.9 nTPM
Tongue	9.6 nTPM
Skin	1.6 nTPM
Prostate	1.5 nTPM
Lung	1.1 nTPM
Vascular	1.1 nTPM
Ovary	0.6 nTPM
Endometrium	0.2 nTPM
Skeletal muscle	0.2 nTPM
Salivary gland	0.2 nTPM
Thymus	0.2 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

Enteroendocrine cells	0.6 nTPM
Rectum	1.7 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM

Fibroblasts	6.9 nTPM
Breast	16.9 nTPM
Adipose tissue	12.2 nTPM
Skin	11.2 nTPM
Skeletal muscle	10.9 nTPM
Stomach	10.1 nTPM
Esophagus	7.5 nTPM
Lung	6.4 nTPM
Thymus	5.5 nTPM
Pancreas	5.1 nTPM
Salivary gland	4.9 nTPM
Fallopian tube	4.9 nTPM
Vascular	4.8 nTPM
Heart muscle	4.2 nTPM
Prostate	3.3 nTPM
Placenta	1.9 nTPM
Liver	0.0 nTPM

Granulocytes	0.5 nTPM
Lung	1.5 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.1 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	17.4 nTPM
Skin	57.9 nTPM
Tongue	43.7 nTPM
Thymus	30.5 nTPM
Fallopian tube	28.7 nTPM
Pancreas	26.7 nTPM
Vascular	22.8 nTPM
Lung	22.4 nTPM
Adipose tissue	20.1 nTPM
Skeletal muscle	19.9 nTPM
Endometrium	17.2 nTPM
Breast	12.6 nTPM
Kidney	9.7 nTPM
Stomach	7.7 nTPM
Salivary gland	6.3 nTPM
Prostate	2.2 nTPM
Bone marrow	1.0 nTPM
Spleen	1.0 nTPM
Testis	0.6 nTPM
Esophagus	0.0 nTPM

Paneth cells	0.2 nTPM
Rectum	0.5 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Basal keratinocytes	14.4 nTPM
Tongue	24.2 nTPM
Skin	4.5 nTPM

Basal prostatic cells	9.3 nTPM
Prostate	9.3 nTPM

Basal respiratory cells	21.1 nTPM
Bronchus	21.1 nTPM

Basal squamous epithelial cells	13.3 nTPM
Esophagus	13.3 nTPM

Plasma cells	0.2 nTPM
Salivary gland	1.3 nTPM
Spleen	0.2 nTPM
Thymus	0.2 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	108.8 nTPM
Adipose tissue	326.0 nTPM
Vascular	0.5 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	4.9 nTPM
Tongue	8.8 nTPM
Salivary gland	0.9 nTPM

Smooth muscle cells	3.4 nTPM
Placenta	10.9 nTPM
Tongue	8.1 nTPM
Endometrium	5.5 nTPM
Vascular	4.1 nTPM
Esophagus	3.6 nTPM
Salivary gland	3.4 nTPM
Thymus	3.3 nTPM
Skin	3.0 nTPM
Breast	2.6 nTPM
Ovary	2.4 nTPM
Adipose tissue	2.2 nTPM
Fallopian tube	1.4 nTPM
Lung	1.2 nTPM
Prostate	1.2 nTPM
Skeletal muscle	1.1 nTPM
Liver	0.4 nTPM

Suprabasal keratinocytes	18.0 nTPM
Tongue	27.7 nTPM
Skin	8.4 nTPM

T-cells	0.8 nTPM
Colon	4.9 nTPM
Tongue	4.8 nTPM
Vascular	2.8 nTPM
Skin	2.5 nTPM
Lung	0.8 nTPM
Prostate	0.6 nTPM
Endometrium	0.5 nTPM
Fallopian tube	0.5 nTPM
Adipose tissue	0.1 nTPM
Breast	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Undifferentiated cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	0.7 nTPM
Hippocampus	1.6 nTPM
Cerebral cortex	1.3 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.4 nTPM
Basal ganglia	0.3 nTPM
Thalamus	0.0 nTPM

Astrocyte	3.9 nTPM
Spinal cord	8.6 nTPM
Hypothalamus	6.3 nTPM
Hippocampus	4.2 nTPM
Medulla oblongata	4.2 nTPM
Cerebellum	4.0 nTPM
Amygdala	3.4 nTPM
Midbrain	3.3 nTPM
Pons	3.1 nTPM
Thalamus	2.6 nTPM
Cerebral cortex	2.1 nTPM
Basal ganglia	1.3 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.3 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	2.6 nTPM
Spinal cord	5.6 nTPM
Amygdala	3.7 nTPM
Cerebellum	2.7 nTPM
Midbrain	2.7 nTPM
Basal ganglia	2.6 nTPM
Hypothalamus	2.4 nTPM
Thalamus	2.1 nTPM
Hippocampus	2.0 nTPM
Pons	1.7 nTPM
Medulla oblongata	1.6 nTPM
Cerebral cortex	1.1 nTPM

Cerebellar inhibitory	0.4 nTPM
Medulla oblongata	0.6 nTPM
Pons	0.5 nTPM
Cerebellum	0.4 nTPM
Midbrain	0.3 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.3 nTPM
Midbrain	0.7 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.1 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Medulla oblongata	0.3 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	10.4 nTPM
Cerebellum	19.0 nTPM
Hippocampus	17.6 nTPM
Cerebral cortex	12.7 nTPM
Basal ganglia	11.5 nTPM
Spinal cord	11.0 nTPM
Midbrain	8.4 nTPM
Medulla oblongata	7.7 nTPM
Hypothalamus	7.5 nTPM
Pons	7.1 nTPM
Amygdala	6.8 nTPM
Thalamus	5.4 nTPM

Deep-layer corticothalamic and 6b	0.1 nTPM
Basal ganglia	0.2 nTPM
Hippocampus	0.2 nTPM
Amygdala	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.4 nTPM
Amygdala	0.5 nTPM
Cerebral cortex	0.5 nTPM
Hippocampus	0.5 nTPM
Basal ganglia	0.3 nTPM
Hypothalamus	0.3 nTPM

Deep-layer near-projecting	0.3 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.4 nTPM
Hippocampus	0.3 nTPM
Cerebral cortex	0.2 nTPM
Basal ganglia	0.0 nTPM

Eccentric medium spiny neuron	0.3 nTPM
Cerebral cortex	0.5 nTPM
Hippocampus	0.4 nTPM
Thalamus	0.4 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.1 nTPM
Hypothalamus	0.1 nTPM

Endothelial cell	0.1 nTPM
Midbrain	0.9 nTPM
Cerebral cortex	0.6 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM