Single cell type - TSC22D4 - The Human Protein Atlas

TSC22D4

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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.	TSC22D4
Gene descriptionⁱ Full gene name according to HGNC.	TSC22 domain family member 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Transcription factors
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.	Muller glia cells - Visual perception (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 (Muller glia 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.	0.47
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.	Cell type enhanced (Bergmann glia, Oligodendrocyte, Astrocyte, 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.	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 (Muller glia 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 (Bergmann glia, Oligodendrocyte, Astrocyte, 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: 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

TSC22D4 is part of cluster 10 Muller glia cells - Visual perception with confidenceⁱ 1
166 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.
CRABP1	Cellular retinoic acid binding protein 1	0.7005	10
MT3	Metallothionein 3	0.6941	10
NPVF	Neuropeptide VF precursor	0.6934	10
LIX1	Limb and CNS expressed 1	0.6870	10
RLBP1	Retinaldehyde binding protein 1	0.6829	10
PRSS35	Serine protease 35	0.6692	10
DIPK1C	Divergent protein kinase domain 1C	0.6681	10
SOX8	SRY-box transcription factor 8	0.6677	10
CLRN1	Clarin 1	0.6611	10
RGR	Retinal G protein coupled receptor	0.6576	10
WIF1	WNT inhibitory factor 1	0.6508	10
FRZB	Frizzled related protein	0.6498	10
SLITRK2	SLIT and NTRK like family member 2	0.6394	10
RAX	Retina and anterior neural fold homeobox	0.6358	10
CA14	Carbonic anhydrase 14	0.6284	10

IMMUNE CELLS

TSC22D4 is part of cluster 36 Eosinophils - Protein ubiquitination with confidenceⁱ 0.82
179 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.
MFNG	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0.9762	36
HINT3	Histidine triad nucleotide binding protein 3	0.9762	36
H2AZ1	H2A.Z variant histone 1	0.9762	25
FBXO38	F-box protein 38	0.9762	36
PDCD6	Programmed cell death 6	0.9524	36
TSSC4	Tumor suppressing subtransferable candidate 4	0.9524	36
CHST13	Carbohydrate sulfotransferase 13	0.9524	36
WDR25	WD repeat domain 25	0.9524	36
ZNF524	Zinc finger protein 524	0.9524	36
UBE2J2	Ubiquitin conjugating enzyme E2 J2	0.9524	36
RNF166	Ring finger protein 166	0.9524	36
PSTPIP2	Proline-serine-threonine phosphatase interacting protein 2	0.9524	25
SAP18	Sin3A associated protein 18	0.9524	36
MMEL1	Membrane metalloendopeptidase like 1	0.9524	25
SUFU	SUFU negative regulator of hedgehog signaling	0.9524	36

Adipocytes	15.9 nTPM
Breast	20.7 nTPM
Adipose tissue	11.1 nTPM

Alveolar cells type 1	24.0 nTPM
Lung	24.0 nTPM

Alveolar cells type 2	23.2 nTPM
Lung	23.2 nTPM

Astrocytes	117.0 nTPM
Brain	117.0 nTPM

B-cells	53.8 nTPM
Esophagus	76.7 nTPM
PBMC	73.9 nTPM
Lung	68.4 nTPM
Kidney	67.6 nTPM
Liver	67.6 nTPM
Skin	61.0 nTPM
Lymph node	55.1 nTPM
Thymus	54.0 nTPM
Spleen	46.7 nTPM
Bone marrow	38.0 nTPM
Stomach	33.3 nTPM
Salivary gland	33.2 nTPM
Adipose tissue	23.5 nTPM

Ciliated cells	19.0 nTPM
Bronchus	23.9 nTPM
Lung	21.8 nTPM
Fallopian tube	16.3 nTPM
Endometrium	13.9 nTPM

Club cells	43.9 nTPM
Bronchus	57.9 nTPM
Prostate	40.5 nTPM
Lung	33.3 nTPM

Dendritic cells	31.1 nTPM
PBMC	39.6 nTPM
Adipose tissue	22.7 nTPM

Endothelial cells	23.6 nTPM
Liver	65.5 nTPM
Breast	48.3 nTPM
Placenta	42.0 nTPM
Ovary	41.6 nTPM
Testis	36.3 nTPM
Pancreas	28.4 nTPM
Endometrium	20.1 nTPM
Skin	17.7 nTPM
Salivary gland	17.2 nTPM
Prostate	17.1 nTPM
Tongue	16.5 nTPM
Vascular	16.1 nTPM
Lung	16.0 nTPM
Thymus	13.4 nTPM
Esophagus	12.6 nTPM
Skeletal muscle	7.6 nTPM
Fallopian tube	5.5 nTPM
Heart muscle	3.3 nTPM

Enteroendocrine cells	33.4 nTPM
Small intestine	41.2 nTPM
Rectum	30.2 nTPM
Colon	28.9 nTPM

Fibroblasts	30.3 nTPM
Placenta	76.8 nTPM
Liver	74.7 nTPM
Pancreas	47.1 nTPM
Adipose tissue	32.9 nTPM
Skin	31.1 nTPM
Breast	27.1 nTPM
Thymus	26.1 nTPM
Skeletal muscle	25.4 nTPM
Salivary gland	23.7 nTPM
Esophagus	22.2 nTPM
Prostate	21.8 nTPM
Fallopian tube	20.7 nTPM
Lung	17.8 nTPM
Stomach	17.3 nTPM
Vascular	16.9 nTPM
Heart muscle	3.0 nTPM

Granulocytes	26.0 nTPM
Lung	46.9 nTPM
Fallopian tube	16.7 nTPM
Tongue	14.6 nTPM

Intestinal goblet cells	34.6 nTPM
Small intestine	49.9 nTPM
Rectum	32.0 nTPM
Colon	21.9 nTPM

Lymphatic endothelial cells	43.9 nTPM
Ovary	70.9 nTPM
Fallopian tube	16.9 nTPM

Macrophages	37.7 nTPM
Pancreas	76.1 nTPM
Lung	54.0 nTPM
Kidney	48.7 nTPM
Stomach	46.3 nTPM
Testis	40.3 nTPM
Thymus	40.2 nTPM
Breast	39.0 nTPM
Fallopian tube	38.7 nTPM
Bone marrow	37.5 nTPM
Spleen	37.1 nTPM
Skin	35.7 nTPM
Skeletal muscle	33.0 nTPM
Salivary gland	30.9 nTPM
Esophagus	30.8 nTPM
Tongue	29.2 nTPM
Adipose tissue	27.3 nTPM
Endometrium	27.1 nTPM
Vascular	25.3 nTPM
Prostate	19.1 nTPM

Basal keratinocytes	29.5 nTPM
Skin	34.9 nTPM
Tongue	24.2 nTPM

Basal prostatic cells	27.7 nTPM
Prostate	27.7 nTPM

Basal squamous epithelial cells	29.9 nTPM
Esophagus	29.9 nTPM

Bipolar cells	12.7 nTPM
Eye	12.7 nTPM

Paneth cells	45.6 nTPM
Small intestine	55.3 nTPM
Rectum	45.4 nTPM
Colon	36.2 nTPM

Plasma cells	30.5 nTPM
Liver	45.1 nTPM
Spleen	39.5 nTPM
Thymus	36.6 nTPM
Stomach	33.5 nTPM
Fallopian tube	30.9 nTPM
Esophagus	26.0 nTPM
Salivary gland	17.0 nTPM
Bone marrow	15.1 nTPM

Schwann cells	177.3 nTPM
Vascular	447.7 nTPM
Esophagus	59.9 nTPM
Adipose tissue	24.2 nTPM

Serous glandular cells	52.6 nTPM
Salivary gland	74.2 nTPM
Tongue	30.9 nTPM

Smooth muscle cells	32.6 nTPM
Placenta	81.0 nTPM
Ovary	50.5 nTPM
Salivary gland	39.6 nTPM
Liver	36.1 nTPM
Adipose tissue	33.8 nTPM
Skin	33.4 nTPM
Skeletal muscle	31.8 nTPM
Lung	31.7 nTPM
Endometrium	31.4 nTPM
Esophagus	30.0 nTPM
Thymus	24.1 nTPM
Tongue	23.1 nTPM
Fallopian tube	20.6 nTPM
Breast	20.4 nTPM
Prostate	18.2 nTPM
Vascular	15.1 nTPM

Suprabasal keratinocytes	39.7 nTPM
Tongue	43.3 nTPM
Skin	36.1 nTPM

T-cells	73.4 nTPM
Liver	134.3 nTPM
Kidney	126.8 nTPM
PBMC	113.2 nTPM
Lung	113.0 nTPM
Skin	102.3 nTPM
Breast	97.4 nTPM
Colon	81.9 nTPM
Thymus	81.9 nTPM
Bone marrow	77.1 nTPM
Esophagus	73.0 nTPM
Skeletal muscle	69.9 nTPM
Spleen	63.5 nTPM
Tongue	60.1 nTPM
Lymph node	54.8 nTPM
Stomach	54.2 nTPM
Adipose tissue	41.7 nTPM
Prostate	41.0 nTPM
Endometrium	40.4 nTPM
Vascular	39.8 nTPM
Fallopian tube	38.0 nTPM
Salivary gland	37.9 nTPM

Undifferentiated cells	27.3 nTPM
Rectum	29.7 nTPM
Small intestine	29.0 nTPM
Colon	23.3 nTPM

Amygdala excitatory	5.0 nTPM
Thalamus	5.9 nTPM
Amygdala	5.8 nTPM
Hypothalamus	5.4 nTPM
Hippocampus	4.7 nTPM
Basal ganglia	4.6 nTPM
Cerebral cortex	3.7 nTPM

Astrocyte	243.3 nTPM
Cerebellum	364.8 nTPM
Pons	327.8 nTPM
Midbrain	276.6 nTPM
Thalamus	252.0 nTPM
Hippocampus	246.2 nTPM
Basal ganglia	242.0 nTPM
Cerebral cortex	236.3 nTPM
Medulla oblongata	235.9 nTPM
Spinal cord	233.0 nTPM
Amygdala	138.9 nTPM
Hypothalamus	123.2 nTPM

Bergmann glia	345.9 nTPM
Pons	404.2 nTPM
Medulla oblongata	347.4 nTPM
Cerebellum	286.2 nTPM

Central nervous system macrophage	50.4 nTPM
Midbrain	61.0 nTPM
Spinal cord	60.1 nTPM
Cerebellum	59.1 nTPM
Hippocampus	58.7 nTPM
Cerebral cortex	52.7 nTPM
Pons	50.8 nTPM
Thalamus	45.1 nTPM
Amygdala	44.4 nTPM
Medulla oblongata	42.7 nTPM
Basal ganglia	41.7 nTPM
Hypothalamus	37.9 nTPM

Cerebellar inhibitory	6.2 nTPM
Pons	8.4 nTPM
Spinal cord	8.2 nTPM
Medulla oblongata	5.9 nTPM
Midbrain	4.4 nTPM
Cerebellum	3.9 nTPM

Cge interneuron	5.9 nTPM
Thalamus	6.4 nTPM
Hippocampus	6.0 nTPM
Hypothalamus	5.9 nTPM
Midbrain	5.9 nTPM
Basal ganglia	5.8 nTPM
Cerebral cortex	5.6 nTPM
Amygdala	5.5 nTPM

Choroid plexus epithelial cell	26.8 nTPM
Thalamus	46.6 nTPM
Basal ganglia	23.0 nTPM
Medulla oblongata	21.1 nTPM
Hippocampus	16.6 nTPM

Committed oligodendrocyte precursor	220.9 nTPM
Spinal cord	331.1 nTPM
Pons	321.4 nTPM
Cerebellum	298.1 nTPM
Midbrain	293.2 nTPM
Hippocampus	212.4 nTPM
Cerebral cortex	206.5 nTPM
Basal ganglia	196.0 nTPM
Medulla oblongata	175.6 nTPM
Thalamus	139.6 nTPM
Amygdala	135.9 nTPM
Hypothalamus	120.2 nTPM

Deep-layer corticothalamic and 6b	4.9 nTPM
Hypothalamus	5.6 nTPM
Cerebral cortex	5.3 nTPM
Basal ganglia	4.9 nTPM
Amygdala	4.8 nTPM
Hippocampus	4.4 nTPM
Midbrain	4.4 nTPM

Deep-layer intratelencephalic	5.9 nTPM
Hypothalamus	6.7 nTPM
Cerebral cortex	6.0 nTPM
Hippocampus	5.8 nTPM
Basal ganglia	5.6 nTPM
Amygdala	5.5 nTPM

Deep-layer near-projecting	3.4 nTPM
Hippocampus	5.5 nTPM
Basal ganglia	3.5 nTPM
Cerebral cortex	3.3 nTPM
Amygdala	2.7 nTPM
Hypothalamus	2.1 nTPM

Eccentric medium spiny neuron	6.9 nTPM
Hippocampus	7.9 nTPM
Cerebral cortex	7.2 nTPM
Thalamus	7.1 nTPM
Hypothalamus	6.8 nTPM
Basal ganglia	6.4 nTPM
Amygdala	6.1 nTPM