Single cell type - TBC1D5 - The Human Protein Atlas

TBC1D5

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(53 genes):

... SKP1 | STAM2 | TBC1D5 | TBL1XR1 | TCAP ...

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.	TBC1D5
Gene descriptionⁱ Full gene name according to HGNC.	TBC1 domain family member 5
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transporters
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.	15

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.	Oligodendrocytes - 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, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Microglial 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.	0.47
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: Group enriched (Oligodendrocytes, Inhibitory neurons, Excitatory neurons, Oligodendrocyte precursor cells, Microglial 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: 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

TBC1D5 is part of cluster 51 Oligodendrocytes - Unknown function with confidenceⁱ 1
302 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.
WDPCP	WD repeat containing planar cell polarity effector	0.7670	51
INVS	Inversin	0.7638	8
HERC3	HECT and RLD domain containing E3 ubiquitin protein ligase 3	0.7177	8
TTLL11	Tubulin tyrosine ligase like 11	0.6859	51
MAGI2	Membrane associated guanylate kinase, WW and PDZ domain containing 2	0.6743	51
ZNF718	Zinc finger protein 718	0.6700	8
RTL4	Retrotransposon Gag like 4	0.6596	51
ENSG00000283765	Novel protein	0.6584	8
WDR7	WD repeat domain 7	0.6392	8
RAPGEF5	Rap guanine nucleotide exchange factor 5	0.6361	51
OR2L13	Olfactory receptor family 2 subfamily L member 13	0.6361	34
RAPGEF6	Rap guanine nucleotide exchange factor 6	0.6322	51
BBS9	Bardet-Biedl syndrome 9	0.6303	51
GRID1	Glutamate ionotropic receptor delta type subunit 1	0.6244	65
AMBRA1	Autophagy and beclin 1 regulator 1	0.6235	51

IMMUNE CELLS

TBC1D5 is part of cluster 24 Non-specific - Transcription with confidenceⁱ 0.77
516 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.
PPP1R3E	Protein phosphatase 1 regulatory subunit 3E	0.9762	12
MTMR9	Myotubularin related protein 9	0.9286	2
HMCES	5-hydroxymethylcytosine binding, ES cell specific	0.9286	14
ZNF772	Zinc finger protein 772	0.9286	24
TRAF3	TNF receptor associated factor 3	0.9048	12
INPP5E	Inositol polyphosphate-5-phosphatase E	0.9048	24
POU2F1	POU class 2 homeobox 1	0.8810	2
ING2	Inhibitor of growth family member 2	0.8810	12
GPR160	G protein-coupled receptor 160	0.8810	24
ENSG00000250264	Novel protein, TAP2-HLA-DOB readthrough	0.8810	2
MT-ND5	Mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5	0.8810	30
H4C14	H4 clustered histone 14	0.8571	24
SEC62	SEC62 homolog, preprotein translocation factor	0.8571	24
H4C15	H4 clustered histone 15	0.8571	24
MT-CO3	Mitochondrially encoded cytochrome c oxidase III	0.8571	30

Adipocytes	38.1 nTPM
Adipose tissue	42.3 nTPM
Breast	33.8 nTPM

Alveolar cells type 1	26.4 nTPM
Lung	26.4 nTPM

Alveolar cells type 2	29.9 nTPM
Lung	29.9 nTPM

B-cells	59.0 nTPM
Esophagus	106.2 nTPM
Lymph node	97.1 nTPM
Bone marrow	92.5 nTPM
Stomach	73.8 nTPM
Spleen	70.1 nTPM
Thymus	64.3 nTPM
Salivary gland	58.4 nTPM
Adipose tissue	46.5 nTPM
PBMC	40.0 nTPM
Lung	33.5 nTPM
Kidney	31.2 nTPM
Skin	28.8 nTPM
Liver	24.2 nTPM

Basal keratinocytes	23.8 nTPM
Tongue	29.1 nTPM
Skin	18.6 nTPM

Ciliated cells	17.4 nTPM
Lung	19.4 nTPM
Endometrium	19.3 nTPM
Fallopian tube	18.5 nTPM
Bronchus	12.4 nTPM

Club cells	25.2 nTPM
Prostate	36.7 nTPM
Lung	27.7 nTPM
Bronchus	11.3 nTPM

Dendritic cells	28.8 nTPM
Adipose tissue	32.5 nTPM
PBMC	25.2 nTPM

Endothelial cells	33.8 nTPM
Vascular	51.9 nTPM
Salivary gland	49.7 nTPM
Esophagus	46.2 nTPM
Tongue	42.7 nTPM
Thymus	40.7 nTPM
Breast	40.4 nTPM
Liver	37.8 nTPM
Prostate	36.4 nTPM
Testis	33.3 nTPM
Skeletal muscle	31.9 nTPM
Fallopian tube	31.3 nTPM
Endometrium	28.4 nTPM
Lung	26.7 nTPM
Ovary	25.3 nTPM
Pancreas	23.3 nTPM
Heart muscle	22.0 nTPM
Placenta	20.4 nTPM
Skin	19.9 nTPM

Enteroendocrine cells	11.3 nTPM
Colon	13.4 nTPM
Small intestine	10.3 nTPM
Rectum	10.1 nTPM

Fibroblasts	32.2 nTPM
Esophagus	52.9 nTPM
Vascular	43.7 nTPM
Adipose tissue	42.6 nTPM
Skeletal muscle	38.8 nTPM
Heart muscle	37.8 nTPM
Salivary gland	37.8 nTPM
Stomach	34.6 nTPM
Prostate	34.3 nTPM
Fallopian tube	33.6 nTPM
Liver	33.2 nTPM
Thymus	29.2 nTPM
Breast	27.9 nTPM
Lung	25.4 nTPM
Skin	21.9 nTPM
Placenta	14.0 nTPM
Pancreas	8.1 nTPM

Granulocytes	26.7 nTPM
Tongue	34.0 nTPM
Fallopian tube	23.6 nTPM
Lung	22.7 nTPM

Intestinal goblet cells	11.1 nTPM
Colon	12.5 nTPM
Rectum	11.8 nTPM
Small intestine	8.9 nTPM

Lymphatic endothelial cells	32.2 nTPM
Fallopian tube	53.5 nTPM
Ovary	10.9 nTPM

Macrophages	39.3 nTPM
Adipose tissue	55.2 nTPM
Salivary gland	54.9 nTPM
Tongue	54.5 nTPM
Stomach	54.0 nTPM
Vascular	51.6 nTPM
Prostate	49.6 nTPM
Spleen	49.1 nTPM
Bone marrow	43.6 nTPM
Skeletal muscle	42.7 nTPM
Fallopian tube	40.5 nTPM
Esophagus	39.8 nTPM
Thymus	39.1 nTPM
Lung	37.3 nTPM
Testis	36.6 nTPM
Endometrium	32.6 nTPM
Breast	30.6 nTPM
Skin	16.7 nTPM
Kidney	9.7 nTPM
Pancreas	8.2 nTPM

Astrocytes	214.9 nTPM
Brain	214.9 nTPM

Bipolar cells	22.5 nTPM
Eye	22.5 nTPM

Collecting duct cells	13.6 nTPM
Kidney	13.6 nTPM

Cone photoreceptor cells	17.0 nTPM
Eye	17.0 nTPM

Paneth cells	7.3 nTPM
Rectum	11.4 nTPM
Small intestine	10.4 nTPM
Colon	0.0 nTPM

Plasma cells	20.3 nTPM
Stomach	26.8 nTPM
Spleen	26.7 nTPM
Fallopian tube	23.8 nTPM
Salivary gland	23.7 nTPM
Thymus	20.7 nTPM
Bone marrow	18.1 nTPM
Liver	12.0 nTPM
Esophagus	10.4 nTPM

Schwann cells	48.2 nTPM
Vascular	51.7 nTPM
Esophagus	47.9 nTPM
Adipose tissue	44.9 nTPM

Serous glandular cells	30.8 nTPM
Salivary gland	35.1 nTPM
Tongue	26.5 nTPM

Smooth muscle cells	24.0 nTPM
Vascular	39.5 nTPM
Tongue	32.9 nTPM
Adipose tissue	30.7 nTPM
Liver	29.7 nTPM
Salivary gland	25.8 nTPM
Skeletal muscle	25.7 nTPM
Endometrium	25.6 nTPM
Prostate	24.9 nTPM
Thymus	24.9 nTPM
Esophagus	24.0 nTPM
Fallopian tube	20.9 nTPM
Ovary	19.4 nTPM
Breast	17.9 nTPM
Skin	14.7 nTPM
Lung	14.1 nTPM
Placenta	13.8 nTPM

Suprabasal keratinocytes	20.4 nTPM
Tongue	23.6 nTPM
Skin	17.1 nTPM

T-cells	31.3 nTPM
Esophagus	53.5 nTPM
Bone marrow	52.9 nTPM
Stomach	43.6 nTPM
Spleen	40.3 nTPM
Lymph node	39.3 nTPM
Vascular	38.6 nTPM
Adipose tissue	34.7 nTPM
Fallopian tube	34.6 nTPM
Thymus	33.8 nTPM
Prostate	33.6 nTPM
Skeletal muscle	31.8 nTPM
Tongue	31.4 nTPM
Salivary gland	29.8 nTPM
Endometrium	29.5 nTPM
Breast	26.1 nTPM
Lung	26.0 nTPM
Liver	22.3 nTPM
PBMC	15.7 nTPM
Skin	14.0 nTPM
Colon	13.6 nTPM
Kidney	11.5 nTPM

Undifferentiated cells	13.9 nTPM
Small intestine	16.7 nTPM
Rectum	14.6 nTPM
Colon	10.4 nTPM

Amygdala excitatory	496.8 nTPM
Hypothalamus	592.0 nTPM
Amygdala	501.9 nTPM
Hippocampus	484.2 nTPM
Thalamus	478.7 nTPM
Basal ganglia	465.1 nTPM
Cerebral cortex	459.0 nTPM

Astrocyte	499.5 nTPM
Amygdala	706.1 nTPM
Hypothalamus	644.6 nTPM
Spinal cord	521.9 nTPM
Basal ganglia	503.3 nTPM
Hippocampus	491.2 nTPM
Cerebral cortex	473.9 nTPM
Thalamus	464.1 nTPM
Midbrain	432.7 nTPM
Medulla oblongata	428.3 nTPM
Pons	422.1 nTPM
Cerebellum	406.4 nTPM

Bergmann glia	425.8 nTPM
Cerebellum	469.0 nTPM
Medulla oblongata	407.0 nTPM
Pons	401.4 nTPM

Central nervous system macrophage	1196.4 nTPM
Amygdala	1842.6 nTPM
Hypothalamus	1432.7 nTPM
Thalamus	1241.1 nTPM
Midbrain	1188.9 nTPM
Hippocampus	1168.7 nTPM
Basal ganglia	1165.3 nTPM
Cerebral cortex	1090.3 nTPM
Cerebellum	1076.7 nTPM
Pons	1075.1 nTPM
Spinal cord	963.2 nTPM
Medulla oblongata	915.8 nTPM

Cerebellar inhibitory	360.1 nTPM
Cerebellum	391.6 nTPM
Midbrain	379.2 nTPM
Medulla oblongata	378.6 nTPM
Pons	345.8 nTPM
Spinal cord	305.2 nTPM

Cge interneuron	348.8 nTPM
Hypothalamus	424.0 nTPM
Amygdala	393.4 nTPM
Thalamus	334.8 nTPM
Hippocampus	334.0 nTPM
Basal ganglia	328.8 nTPM
Cerebral cortex	317.4 nTPM
Midbrain	308.9 nTPM

Choroid plexus epithelial cell	421.5 nTPM
Basal ganglia	586.1 nTPM
Medulla oblongata	413.4 nTPM
Hippocampus	363.3 nTPM
Thalamus	323.4 nTPM

Committed oligodendrocyte precursor	579.7 nTPM
Amygdala	770.2 nTPM
Hypothalamus	757.9 nTPM
Basal ganglia	616.5 nTPM
Thalamus	600.9 nTPM
Hippocampus	597.3 nTPM
Cerebral cortex	587.7 nTPM
Cerebellum	569.2 nTPM
Midbrain	556.1 nTPM
Spinal cord	478.3 nTPM
Pons	457.7 nTPM
Medulla oblongata	384.7 nTPM

Deep-layer corticothalamic and 6b	409.7 nTPM
Hypothalamus	492.6 nTPM
Amygdala	434.5 nTPM
Hippocampus	434.2 nTPM
Cerebral cortex	396.7 nTPM
Basal ganglia	350.9 nTPM
Midbrain	349.5 nTPM

Deep-layer intratelencephalic	448.7 nTPM
Hypothalamus	519.3 nTPM
Amygdala	477.7 nTPM
Hippocampus	448.0 nTPM
Cerebral cortex	400.6 nTPM
Basal ganglia	397.8 nTPM

Deep-layer near-projecting	504.4 nTPM
Hypothalamus	594.4 nTPM
Amygdala	549.4 nTPM
Cerebral cortex	490.5 nTPM
Basal ganglia	452.1 nTPM
Hippocampus	435.8 nTPM

Eccentric medium spiny neuron	483.9 nTPM
Hypothalamus	514.9 nTPM
Amygdala	511.7 nTPM
Thalamus	489.8 nTPM
Hippocampus	486.2 nTPM
Basal ganglia	457.1 nTPM
Cerebral cortex	443.6 nTPM