Single cell type - IL7 - The Human Protein Atlas

IL7

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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.	IL7
Gene descriptionⁱ Full gene name according to HGNC.	Interleukin 7
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes 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.	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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.	Late spermatids - 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 (Late spermatids, Early spermatids, Lymphatic endothelial 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.	0.77
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.	Immune cell enhanced (memory B-cell, naive B-cell)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data.	Protein predicted to be secreted

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 (Late spermatids, Early spermatids, Lymphatic endothelial 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: Immune cell enhanced (memory B-cell, naive B-cell)
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

IL7 is part of cluster 36 Late spermatids - Unknown function with confidenceⁱ 1
427 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.
TBX1	T-box transcription factor 1	0.7283	54
ENSG00000275778	PRH1-PRR4 readthrough	0.6492	36
DUXB	Double homeobox B	0.6137	54
KRTAP26-1	Keratin associated protein 26-1	0.6032	36
OR5C1	Olfactory receptor family 5 subfamily C member 1	0.6006	36
KIF17	Kinesin family member 17	0.5878	36
SLC25A46	Solute carrier family 25 member 46	0.5648	36
ENSG00000286022	Novel protein	0.5564	36
OTOP1	Otopetrin 1	0.5510	36
FAM163A	Family with sequence similarity 163 member A	0.5507	36
SLC22A14	Solute carrier family 22 member 14	0.5490	36
FANCM	FA complementation group M	0.5489	36
TPP2	Tripeptidyl peptidase 2	0.5450	36
EFCC1	EF-hand and coiled-coil domain containing 1	0.5362	54
PRY2	PTPN13 like Y-linked 2	0.5310	36

IMMUNE CELLS

IL7 is part of cluster 32 Basophils - Transcription with confidenceⁱ 0.95
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.
TENT5C	Terminal nucleotidyltransferase 5C	0.9524	32
PPOX	Protoporphyrinogen oxidase	0.9048	5
DMD	Dystrophin	0.9048	32
ZNF257	Zinc finger protein 257	0.9048	32
NPIPA1	Nuclear pore complex interacting protein family member A1	0.9048	32
ZNF581	Zinc finger protein 581	0.9048	32
PLPP5	Phospholipid phosphatase 5	0.9048	32
SOX30	SRY-box transcription factor 30	0.9048	5
DYNC2LI1	Dynein cytoplasmic 2 light intermediate chain 1	0.9048	32
BRIP1	BRCA1 interacting helicase 1	0.9048	16
TNRC6A	Trinucleotide repeat containing adaptor 6A	0.9048	32
NUF2	NUF2 component of NDC80 kinetochore complex	0.8810	5
CEP164	Centrosomal protein 164	0.8810	32
ARID5B	AT-rich interaction domain 5B	0.8810	16
ITPR1	Inositol 1,4,5-trisphosphate receptor type 1	0.8810	32

Adipocytes	0.4 nTPM
Adipose tissue	0.4 nTPM
Breast	0.4 nTPM

Alveolar cells type 1	0.7 nTPM
Lung	0.7 nTPM

Alveolar cells type 2	2.5 nTPM
Lung	2.5 nTPM

Astrocytes	5.6 nTPM
Brain	5.6 nTPM

B-cells	9.6 nTPM
PBMC	21.6 nTPM
Stomach	15.2 nTPM
Bone marrow	13.8 nTPM
Spleen	12.8 nTPM
Esophagus	11.8 nTPM
Lymph node	11.5 nTPM
Liver	9.7 nTPM
Thymus	8.0 nTPM
Adipose tissue	6.6 nTPM
Salivary gland	6.0 nTPM
Kidney	5.2 nTPM
Skin	1.7 nTPM
Lung	1.3 nTPM

Ciliated cells	16.2 nTPM
Endometrium	23.0 nTPM
Lung	20.1 nTPM
Fallopian tube	17.5 nTPM
Bronchus	4.1 nTPM

Club cells	2.3 nTPM
Lung	2.9 nTPM
Prostate	2.8 nTPM
Bronchus	1.1 nTPM

Endothelial cells	5.8 nTPM
Breast	71.2 nTPM
Esophagus	5.4 nTPM
Salivary gland	5.0 nTPM
Placenta	4.0 nTPM
Lung	3.6 nTPM
Thymus	2.9 nTPM
Prostate	2.2 nTPM
Tongue	2.0 nTPM
Testis	1.8 nTPM
Skeletal muscle	1.4 nTPM
Vascular	1.4 nTPM
Heart muscle	1.3 nTPM
Fallopian tube	1.2 nTPM
Endometrium	0.8 nTPM
Skin	0.4 nTPM
Ovary	0.3 nTPM
Liver	0.0 nTPM
Pancreas	0.0 nTPM

Enteroendocrine cells	4.6 nTPM
Small intestine	6.9 nTPM
Colon	5.3 nTPM
Rectum	1.7 nTPM

Fibroblasts	2.2 nTPM
Skin	8.4 nTPM
Stomach	4.3 nTPM
Esophagus	3.5 nTPM
Adipose tissue	3.3 nTPM
Salivary gland	2.9 nTPM
Lung	2.6 nTPM
Pancreas	1.7 nTPM
Breast	1.6 nTPM
Skeletal muscle	1.5 nTPM
Vascular	1.3 nTPM
Fallopian tube	1.3 nTPM
Liver	1.2 nTPM
Thymus	0.9 nTPM
Prostate	0.7 nTPM
Heart muscle	0.0 nTPM
Placenta	0.0 nTPM

Granulocytes	0.1 nTPM
Fallopian tube	0.2 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	6.2 nTPM
Small intestine	9.2 nTPM
Rectum	5.6 nTPM
Colon	3.7 nTPM

Lymphatic endothelial cells	37.9 nTPM
Fallopian tube	53.9 nTPM
Ovary	21.8 nTPM

Macrophages	2.2 nTPM
Stomach	5.1 nTPM
Vascular	4.7 nTPM
Testis	3.1 nTPM
Breast	2.9 nTPM
Tongue	2.8 nTPM
Kidney	2.7 nTPM
Lung	2.7 nTPM
Adipose tissue	2.6 nTPM
Fallopian tube	2.3 nTPM
Skin	2.2 nTPM
Pancreas	2.1 nTPM
Spleen	2.0 nTPM
Skeletal muscle	1.7 nTPM
Endometrium	1.2 nTPM
Bone marrow	1.0 nTPM
Thymus	0.8 nTPM
Prostate	0.7 nTPM
Salivary gland	0.5 nTPM
Esophagus	0.0 nTPM

Paneth cells	13.1 nTPM
Colon	14.5 nTPM
Rectum	14.3 nTPM
Small intestine	10.4 nTPM

Basal squamous epithelial cells	8.2 nTPM
Esophagus	8.2 nTPM

Cholangiocytes	3.8 nTPM
Liver	3.8 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Distal enterocytes	7.4 nTPM
Colon	8.6 nTPM
Rectum	6.3 nTPM

Plasma cells	0.5 nTPM
Bone marrow	1.5 nTPM
Stomach	0.8 nTPM
Liver	0.5 nTPM
Spleen	0.5 nTPM
Thymus	0.3 nTPM
Esophagus	0.0 nTPM
Salivary gland	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.1 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.7 nTPM
Salivary gland	1.5 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.8 nTPM
Liver	2.1 nTPM
Tongue	2.1 nTPM
Breast	1.4 nTPM
Esophagus	1.2 nTPM
Lung	1.2 nTPM
Skin	0.9 nTPM
Salivary gland	0.8 nTPM
Thymus	0.7 nTPM
Vascular	0.7 nTPM
Endometrium	0.6 nTPM
Fallopian tube	0.5 nTPM
Placenta	0.4 nTPM
Ovary	0.3 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.0 nTPM
Prostate	0.0 nTPM

T-cells	1.2 nTPM
Kidney	5.3 nTPM
Stomach	2.5 nTPM
Adipose tissue	1.8 nTPM
Bone marrow	1.8 nTPM
Tongue	1.7 nTPM
Skeletal muscle	1.5 nTPM
Breast	1.5 nTPM
Lung	1.3 nTPM
Lymph node	1.2 nTPM
Vascular	1.2 nTPM
Liver	1.1 nTPM
PBMC	1.1 nTPM
Skin	1.1 nTPM
Colon	1.0 nTPM
Spleen	0.7 nTPM
Fallopian tube	0.5 nTPM
Thymus	0.3 nTPM
Endometrium	0.2 nTPM
Esophagus	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM

Undifferentiated cells	4.6 nTPM
Small intestine	6.8 nTPM
Rectum	3.6 nTPM
Colon	3.4 nTPM

Amygdala excitatory	29.4 nTPM
Thalamus	45.4 nTPM
Cerebral cortex	40.5 nTPM
Basal ganglia	37.4 nTPM
Amygdala	25.6 nTPM
Hippocampus	22.1 nTPM
Hypothalamus	5.4 nTPM

Astrocyte	40.0 nTPM
Hypothalamus	167.6 nTPM
Medulla oblongata	45.8 nTPM
Basal ganglia	44.6 nTPM
Amygdala	38.7 nTPM
Thalamus	27.8 nTPM
Hippocampus	25.2 nTPM
Cerebral cortex	22.7 nTPM
Midbrain	21.6 nTPM
Pons	20.8 nTPM
Spinal cord	16.2 nTPM
Cerebellum	9.2 nTPM

Bergmann glia	52.1 nTPM
Medulla oblongata	89.5 nTPM
Pons	38.8 nTPM
Cerebellum	28.0 nTPM

Central nervous system macrophage	24.3 nTPM
Hypothalamus	69.8 nTPM
Medulla oblongata	35.6 nTPM
Basal ganglia	32.8 nTPM
Thalamus	23.8 nTPM
Pons	22.4 nTPM
Spinal cord	18.3 nTPM
Cerebellum	16.2 nTPM
Amygdala	13.7 nTPM
Midbrain	13.6 nTPM
Cerebral cortex	12.0 nTPM
Hippocampus	8.9 nTPM

Cerebellar inhibitory	18.7 nTPM
Pons	32.3 nTPM
Medulla oblongata	28.4 nTPM
Midbrain	20.2 nTPM
Cerebellum	9.9 nTPM
Spinal cord	2.7 nTPM

Cge interneuron	17.2 nTPM
Hippocampus	27.1 nTPM
Basal ganglia	20.5 nTPM
Midbrain	19.7 nTPM
Cerebral cortex	18.6 nTPM
Amygdala	18.2 nTPM
Thalamus	13.0 nTPM
Hypothalamus	3.6 nTPM

Choroid plexus epithelial cell	14.3 nTPM
Hippocampus	30.5 nTPM
Medulla oblongata	15.5 nTPM
Thalamus	8.2 nTPM
Basal ganglia	3.1 nTPM

Committed oligodendrocyte precursor	14.6 nTPM
Medulla oblongata	21.9 nTPM
Midbrain	19.3 nTPM
Cerebellum	19.0 nTPM
Hypothalamus	18.4 nTPM
Pons	16.8 nTPM
Spinal cord	14.7 nTPM
Thalamus	14.0 nTPM
Basal ganglia	11.0 nTPM
Hippocampus	9.1 nTPM
Cerebral cortex	8.9 nTPM
Amygdala	7.9 nTPM

Deep-layer corticothalamic and 6b	42.7 nTPM
Hippocampus	55.8 nTPM
Basal ganglia	54.0 nTPM
Midbrain	51.0 nTPM
Amygdala	46.9 nTPM
Cerebral cortex	46.0 nTPM
Hypothalamus	2.7 nTPM

Deep-layer intratelencephalic	34.2 nTPM
Basal ganglia	48.2 nTPM
Hippocampus	45.3 nTPM
Amygdala	39.0 nTPM
Cerebral cortex	36.7 nTPM
Hypothalamus	1.9 nTPM

Deep-layer near-projecting	38.2 nTPM
Hippocampus	77.7 nTPM
Basal ganglia	42.6 nTPM
Amygdala	40.0 nTPM
Cerebral cortex	29.5 nTPM
Hypothalamus	1.5 nTPM

Eccentric medium spiny neuron	39.3 nTPM
Hippocampus	70.5 nTPM
Amygdala	51.7 nTPM
Cerebral cortex	38.4 nTPM
Thalamus	28.5 nTPM
Basal ganglia	26.7 nTPM
Hypothalamus	19.8 nTPM

Endothelial cell	12.6 nTPM
Hypothalamus	28.5 nTPM
Amygdala	23.5 nTPM
Hippocampus	11.9 nTPM
Medulla oblongata	11.3 nTPM
Midbrain	11.3 nTPM
Thalamus	11.3 nTPM
Cerebellum	10.8 nTPM
Basal ganglia	10.3 nTPM
Cerebral cortex	8.3 nTPM
Pons	7.5 nTPM
Spinal cord	3.5 nTPM

Ependymal cell	57.2 nTPM
Hypothalamus	132.1 nTPM
Thalamus	68.0 nTPM
Medulla oblongata	63.7 nTPM
Hippocampus	57.5 nTPM
Basal ganglia	45.0 nTPM
Amygdala	44.9 nTPM
Midbrain	42.5 nTPM
Pons	40.1 nTPM
Spinal cord	21.1 nTPM