Single cell type - TNFSF9 - The Human Protein Atlas

TNFSF9

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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.	TNFSF9
Gene descriptionⁱ Full gene name according to HGNC.	TNF superfamily member 9
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.	1

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.	NK-cells & T-cells - Immune system & Transcription (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 (Dendritic cells, B-cells, Schwann cells, Alveolar cells type 2, T-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.	0.69
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.	Not detected in immune cells
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 (Dendritic cells, B-cells, Schwann cells, Alveolar cells type 2, T-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: 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: Not detected in immune cells
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

TNFSF9 is part of cluster 78 NK-cells & T-cells - Immune system & Transcription with confidenceⁱ 1
392 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.
CXCR4	C-X-C motif chemokine receptor 4	0.7272	78
EZR	Ezrin	0.6739	78
JUND	JunD proto-oncogene, AP-1 transcription factor subunit	0.6414	78
RBM38	RNA binding motif protein 38	0.6255	78
STK4	Serine/threonine kinase 4	0.6203	78
DUSP2	Dual specificity phosphatase 2	0.6165	78
ARL4C	ADP ribosylation factor like GTPase 4C	0.6084	78
GTF2B	General transcription factor IIB	0.6004	80
POLR2A	RNA polymerase II subunit A	0.5849	80
ZBTB1	Zinc finger and BTB domain containing 1	0.5758	78
SRSF7	Serine and arginine rich splicing factor 7	0.5726	80
G3BP2	G3BP stress granule assembly factor 2	0.5574	78
TIPARP	TCDD inducible poly(ADP-ribose) polymerase	0.5554	29
RGS1	Regulator of G protein signaling 1	0.5553	28
METRNL	Meteorin like, glial cell differentiation regulator	0.5550	78

IMMUNE CELLS

TNFSF9 is part of cluster 14 Non-specific - Unknown function with confidenceⁱ 1
292 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.
LEKR1	Leucine, glutamate and lysine rich 1	1.0000	14
RRAS2	RAS related 2	0.9762	14
BICD1	BICD cargo adaptor 1	0.9762	14
DISP1	Dispatched RND transporter family member 1	0.9762	14
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	0.9762	14
CXXC5	CXXC finger protein 5	0.9762	14
AUTS2	Activator of transcription and developmental regulator AUTS2	0.9524	14
L3MBTL3	L3MBTL histone methyl-lysine binding protein 3	0.9524	14
AIDA	Axin interactor, dorsalization associated	0.9524	14
C19orf18	Chromosome 19 open reading frame 18	0.9524	14
DOK7	Docking protein 7	0.9524	14
AK8	Adenylate kinase 8	0.9524	14
STRBP	Spermatid perinuclear RNA binding protein	0.9524	14
RPL22L1	Ribosomal protein L22 like 1	0.9524	14
APOBEC2	Apolipoprotein B mRNA editing enzyme catalytic subunit 2	0.9524	14

Adipocytes	9.1 nTPM
Adipose tissue	12.5 nTPM
Breast	5.8 nTPM

Alveolar cells type 1	18.4 nTPM
Lung	18.4 nTPM

Alveolar cells type 2	45.7 nTPM
Lung	45.7 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	51.8 nTPM
Adipose tissue	181.5 nTPM
Thymus	150.6 nTPM
Stomach	71.3 nTPM
Spleen	60.6 nTPM
Lymph node	55.3 nTPM
Esophagus	47.2 nTPM
Skin	33.9 nTPM
Liver	24.2 nTPM
Salivary gland	20.0 nTPM
Lung	18.8 nTPM
Bone marrow	9.7 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM

Ciliated cells	4.8 nTPM
Fallopian tube	10.1 nTPM
Endometrium	5.3 nTPM
Lung	2.6 nTPM
Bronchus	1.2 nTPM

Club cells	5.0 nTPM
Lung	10.9 nTPM
Bronchus	2.5 nTPM
Prostate	1.7 nTPM

Dendritic cells	78.6 nTPM
Adipose tissue	150.1 nTPM
PBMC	7.2 nTPM

Endothelial cells	14.5 nTPM
Vascular	59.3 nTPM
Fallopian tube	50.1 nTPM
Skin	31.1 nTPM
Tongue	25.9 nTPM
Esophagus	18.6 nTPM
Prostate	18.3 nTPM
Thymus	13.0 nTPM
Endometrium	10.8 nTPM
Salivary gland	10.3 nTPM
Lung	9.3 nTPM
Heart muscle	5.7 nTPM
Skeletal muscle	3.9 nTPM
Breast	3.5 nTPM
Placenta	0.6 nTPM
Ovary	0.6 nTPM
Testis	0.0 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	3.0 nTPM
Colon	9.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	11.7 nTPM
Adipose tissue	51.6 nTPM
Stomach	31.7 nTPM
Vascular	24.3 nTPM
Esophagus	15.7 nTPM
Thymus	13.3 nTPM
Skin	10.2 nTPM
Skeletal muscle	7.5 nTPM
Lung	7.3 nTPM
Fallopian tube	6.9 nTPM
Heart muscle	5.7 nTPM
Prostate	4.6 nTPM
Breast	4.1 nTPM
Salivary gland	3.6 nTPM
Pancreas	0.6 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM

Granulocytes	11.0 nTPM
Tongue	24.3 nTPM
Fallopian tube	4.6 nTPM
Lung	4.0 nTPM

Intestinal goblet cells	3.5 nTPM
Colon	8.9 nTPM
Rectum	1.5 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	4.1 nTPM
Fallopian tube	8.2 nTPM
Ovary	0.0 nTPM

Macrophages	26.6 nTPM
Adipose tissue	134.3 nTPM
Breast	65.9 nTPM
Fallopian tube	61.0 nTPM
Vascular	59.8 nTPM
Endometrium	35.1 nTPM
Tongue	28.6 nTPM
Prostate	25.3 nTPM
Skin	21.2 nTPM
Esophagus	19.3 nTPM
Pancreas	10.3 nTPM
Lung	9.2 nTPM
Thymus	8.4 nTPM
Spleen	8.0 nTPM
Salivary gland	7.4 nTPM
Skeletal muscle	5.3 nTPM
Stomach	5.1 nTPM
Bone marrow	2.0 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM

Basal prostatic cells	4.2 nTPM
Prostate	4.2 nTPM

Basal squamous epithelial cells	6.2 nTPM
Esophagus	6.2 nTPM

Bipolar cells	0.5 nTPM
Eye	0.5 nTPM

Paneth cells	0.3 nTPM
Rectum	1.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	13.9 nTPM
Esophagus	41.6 nTPM
Stomach	17.6 nTPM
Thymus	17.1 nTPM
Spleen	11.3 nTPM
Fallopian tube	9.6 nTPM
Salivary gland	8.1 nTPM
Liver	4.5 nTPM
Bone marrow	1.5 nTPM

Schwann cells	51.6 nTPM
Adipose tissue	147.6 nTPM
Vascular	7.3 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	11.5 nTPM
Tongue	22.1 nTPM
Salivary gland	0.8 nTPM

Smooth muscle cells	7.3 nTPM
Adipose tissue	29.6 nTPM
Esophagus	13.2 nTPM
Tongue	11.4 nTPM
Fallopian tube	10.1 nTPM
Skin	7.2 nTPM
Lung	7.1 nTPM
Endometrium	7.0 nTPM
Breast	6.9 nTPM
Vascular	5.7 nTPM
Thymus	5.2 nTPM
Skeletal muscle	5.1 nTPM
Prostate	4.3 nTPM
Salivary gland	2.4 nTPM
Ovary	1.9 nTPM
Liver	0.4 nTPM
Placenta	0.3 nTPM

Suprabasal keratinocytes	31.5 nTPM
Tongue	61.7 nTPM
Skin	1.3 nTPM

T-cells	43.3 nTPM
Prostate	112.4 nTPM
Breast	103.0 nTPM
Adipose tissue	95.9 nTPM
Vascular	92.5 nTPM
Colon	82.9 nTPM
Tongue	70.1 nTPM
Spleen	63.1 nTPM
Fallopian tube	61.3 nTPM
Thymus	35.6 nTPM
Esophagus	34.1 nTPM
Stomach	29.9 nTPM
Lung	29.0 nTPM
Skin	27.3 nTPM
Endometrium	26.5 nTPM
Skeletal muscle	16.6 nTPM
Lymph node	13.3 nTPM
Salivary gland	8.1 nTPM
Bone marrow	6.3 nTPM
Liver	2.4 nTPM
PBMC	0.1 nTPM
Kidney	0.0 nTPM

Undifferentiated cells	7.2 nTPM
Colon	20.1 nTPM
Rectum	1.2 nTPM
Small intestine	0.4 nTPM

Amygdala excitatory	2.3 nTPM
Amygdala	2.8 nTPM
Hippocampus	2.7 nTPM
Cerebral cortex	2.5 nTPM
Thalamus	2.3 nTPM
Basal ganglia	1.7 nTPM
Hypothalamus	1.5 nTPM

Astrocyte	0.2 nTPM
Medulla oblongata	0.3 nTPM
Midbrain	0.3 nTPM
Amygdala	0.2 nTPM
Hypothalamus	0.2 nTPM
Thalamus	0.2 nTPM
Basal ganglia	0.1 nTPM
Cerebellum	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Pons	0.1 nTPM
Spinal cord	0.1 nTPM

Bergmann glia	0.1 nTPM
Cerebellum	0.2 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.5 nTPM
Hypothalamus	1.0 nTPM
Medulla oblongata	1.0 nTPM
Spinal cord	0.6 nTPM
Cerebral cortex	0.5 nTPM
Pons	0.5 nTPM
Thalamus	0.5 nTPM
Hippocampus	0.4 nTPM
Amygdala	0.2 nTPM
Basal ganglia	0.2 nTPM
Midbrain	0.1 nTPM
Cerebellum	0.0 nTPM

Cerebellar inhibitory	0.8 nTPM
Pons	2.1 nTPM
Midbrain	0.9 nTPM
Medulla oblongata	0.6 nTPM
Cerebellum	0.3 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	4.0 nTPM
Midbrain	5.4 nTPM
Basal ganglia	4.8 nTPM
Cerebral cortex	4.5 nTPM
Hippocampus	3.7 nTPM
Amygdala	3.5 nTPM
Thalamus	3.4 nTPM
Hypothalamus	2.9 nTPM

Choroid plexus epithelial cell	1.4 nTPM
Hippocampus	5.5 nTPM
Basal ganglia	0.1 nTPM
Medulla oblongata	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	2.0 nTPM
Midbrain	4.2 nTPM
Cerebellum	3.2 nTPM
Cerebral cortex	3.2 nTPM
Basal ganglia	2.7 nTPM
Medulla oblongata	2.6 nTPM
Hippocampus	2.1 nTPM
Pons	1.8 nTPM
Hypothalamus	1.4 nTPM
Thalamus	0.9 nTPM
Amygdala	0.6 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	3.0 nTPM
Hippocampus	3.3 nTPM
Midbrain	3.3 nTPM
Basal ganglia	3.2 nTPM
Cerebral cortex	3.1 nTPM
Amygdala	2.9 nTPM
Hypothalamus	2.2 nTPM

Deep-layer intratelencephalic	2.9 nTPM
Cerebral cortex	3.5 nTPM
Hippocampus	3.1 nTPM
Basal ganglia	2.9 nTPM
Amygdala	2.5 nTPM
Hypothalamus	2.5 nTPM

Deep-layer near-projecting	4.1 nTPM
Hippocampus	6.5 nTPM
Cerebral cortex	4.1 nTPM
Basal ganglia	3.8 nTPM
Amygdala	3.6 nTPM
Hypothalamus	2.6 nTPM

Eccentric medium spiny neuron	2.1 nTPM
Hippocampus	3.7 nTPM
Amygdala	2.2 nTPM
Cerebral cortex	2.2 nTPM
Basal ganglia	1.7 nTPM
Thalamus	1.5 nTPM
Hypothalamus	1.4 nTPM