Single cell type - ID3 - The Human Protein Atlas

ID3

Search result

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.	ID3
Gene descriptionⁱ Full gene name according to HGNC.	Inhibitor of DNA binding 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes 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.	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.	Adipocytes & Endothelial cells - Mixed 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.	Cell type enhanced (Adipocytes, Extravillous trophoblasts, Basal respiratory 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.	0.41
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 (Endothelial cell, Vascular associated smooth muscle cell, Astrocyte)
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

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 (Adipocytes, Extravillous trophoblasts, Basal respiratory 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 (Endothelial cell, Vascular associated smooth muscle cell, Astrocyte)

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

ID3 is part of cluster 41 Adipocytes & Endothelial cells - Mixed function with confidenceⁱ 1
325 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.
ID1	Inhibitor of DNA binding 1	0.8263	41
SNAI1	Snail family transcriptional repressor 1	0.6490	80
TNFRSF10D	TNF receptor superfamily member 10d	0.6431	41
DLL1	Delta like canonical Notch ligand 1	0.6199	16
APLNR	Apelin receptor	0.6034	41
MEOX1	Mesenchyme homeobox 1	0.6002	41
DLL4	Delta like canonical Notch ligand 4	0.5850	41
PLK2	Polo like kinase 2	0.5715	80
BDKRB2	Bradykinin receptor B2	0.5587	41
ADM5	Adrenomedullin 5 (putative)	0.5561	41
PLVAP	Plasmalemma vesicle associated protein	0.5545	41
GPIHBP1	Glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	0.5485	41
SOX7	SRY-box transcription factor 7	0.5441	41
FLYWCH2	FLYWCH family member 2	0.5421	79
ZNF442	Zinc finger protein 442	0.5403	80

IMMUNE CELLS

ID3 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.98
433 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.
ENSG00000281179	Novel gene identicle to IGHV1OR15-1	1.0000	43
IGHV1OR15-1	Immunoglobulin heavy variable 1/OR15-1 (non-functional)	1.0000	43
H3C3	H3 clustered histone 3	0.9762	43
SNX25	Sorting nexin 25	0.9762	43
GJB6	Gap junction protein beta 6	0.9762	43
H2AC11	H2A clustered histone 11	0.9762	43
PDE4DIP	Phosphodiesterase 4D interacting protein	0.9762	43
FCMR	Fc mu receptor	0.9762	43
IGSF8	Immunoglobulin superfamily member 8	0.9524	43
GRAP	GRB2 related adaptor protein	0.9524	43
CHMP7	Charged multivesicular body protein 7	0.9524	43
GNB5	G protein subunit beta 5	0.9524	43
DMRTC1B	DMRT like family C1B	0.9286	43
PRPSAP2	Phosphoribosyl pyrophosphate synthetase associated protein 2	0.9286	43
ZNF607	Zinc finger protein 607	0.9286	43

Adipocytes	1604.5 nTPM
Breast	2130.2 nTPM
Adipose tissue	1078.7 nTPM

Alveolar cells type 1	133.7 nTPM
Lung	133.7 nTPM

Alveolar cells type 2	157.4 nTPM
Lung	157.4 nTPM

Astrocytes	73.7 nTPM
Brain	73.7 nTPM

B-cells	186.8 nTPM
Lymph node	671.5 nTPM
Esophagus	477.9 nTPM
Kidney	254.8 nTPM
PBMC	135.5 nTPM
Liver	135.2 nTPM
Lung	134.1 nTPM
Spleen	118.9 nTPM
Skin	113.5 nTPM
Stomach	100.0 nTPM
Adipose tissue	97.1 nTPM
Bone marrow	92.5 nTPM
Thymus	60.4 nTPM
Salivary gland	36.8 nTPM

Basal squamous epithelial cells	468.5 nTPM
Esophagus	468.5 nTPM

Ciliated cells	234.9 nTPM
Endometrium	532.1 nTPM
Bronchus	190.7 nTPM
Fallopian tube	167.3 nTPM
Lung	49.4 nTPM

Club cells	273.8 nTPM
Bronchus	492.2 nTPM
Prostate	274.1 nTPM
Lung	55.0 nTPM

Endothelial cells	873.7 nTPM
Esophagus	2310.5 nTPM
Fallopian tube	1763.4 nTPM
Endometrium	1381.9 nTPM
Skeletal muscle	1285.9 nTPM
Pancreas	1142.7 nTPM
Breast	881.4 nTPM
Testis	845.5 nTPM
Placenta	743.7 nTPM
Liver	736.9 nTPM
Thymus	714.6 nTPM
Skin	642.9 nTPM
Ovary	607.1 nTPM
Vascular	578.8 nTPM
Heart muscle	509.1 nTPM
Prostate	493.6 nTPM
Tongue	435.5 nTPM
Lung	379.4 nTPM
Salivary gland	273.4 nTPM

Enteroendocrine cells	706.7 nTPM
Colon	1061.4 nTPM
Small intestine	600.8 nTPM
Rectum	457.9 nTPM

Fibroblasts	597.6 nTPM
Pancreas	1435.7 nTPM
Skin	1194.2 nTPM
Liver	1112.4 nTPM
Fallopian tube	1106.3 nTPM
Stomach	892.0 nTPM
Esophagus	696.2 nTPM
Thymus	588.1 nTPM
Breast	472.6 nTPM
Prostate	431.0 nTPM
Skeletal muscle	396.2 nTPM
Adipose tissue	298.4 nTPM
Lung	253.4 nTPM
Vascular	208.7 nTPM
Heart muscle	199.2 nTPM
Salivary gland	170.3 nTPM
Placenta	107.6 nTPM

Granulocytes	46.9 nTPM
Tongue	82.5 nTPM
Fallopian tube	46.7 nTPM
Lung	11.6 nTPM

Intestinal goblet cells	804.9 nTPM
Colon	1240.6 nTPM
Small intestine	861.2 nTPM
Rectum	312.7 nTPM

Lymphatic endothelial cells	159.8 nTPM
Fallopian tube	259.6 nTPM
Ovary	60.0 nTPM

Macrophages	82.9 nTPM
Breast	346.7 nTPM
Pancreas	180.9 nTPM
Esophagus	176.0 nTPM
Endometrium	147.0 nTPM
Tongue	117.2 nTPM
Prostate	114.5 nTPM
Skin	95.8 nTPM
Lung	88.7 nTPM
Thymus	72.3 nTPM
Adipose tissue	54.0 nTPM
Fallopian tube	42.2 nTPM
Skeletal muscle	40.5 nTPM
Vascular	31.1 nTPM
Kidney	29.2 nTPM
Testis	13.6 nTPM
Spleen	9.0 nTPM
Salivary gland	8.1 nTPM
Stomach	5.1 nTPM
Bone marrow	3.0 nTPM

Bipolar cells	11.0 nTPM
Eye	11.0 nTPM

Cholangiocytes	17.2 nTPM
Liver	17.2 nTPM

Collecting duct cells	178.9 nTPM
Kidney	178.9 nTPM

Cone photoreceptor cells	3.4 nTPM
Eye	3.4 nTPM

Paneth cells	655.6 nTPM
Colon	1172.4 nTPM
Small intestine	431.7 nTPM
Rectum	362.6 nTPM

Plasma cells	67.3 nTPM
Esophagus	265.1 nTPM
Stomach	113.9 nTPM
Fallopian tube	76.6 nTPM
Salivary gland	26.0 nTPM
Thymus	19.9 nTPM
Liver	19.0 nTPM
Bone marrow	10.6 nTPM
Spleen	7.7 nTPM

Schwann cells	252.0 nTPM
Esophagus	611.0 nTPM
Vascular	139.5 nTPM
Adipose tissue	5.5 nTPM

Serous glandular cells	66.7 nTPM
Tongue	123.7 nTPM
Salivary gland	9.7 nTPM

Smooth muscle cells	681.0 nTPM
Liver	1909.5 nTPM
Esophagus	1601.3 nTPM
Fallopian tube	782.0 nTPM
Breast	777.4 nTPM
Ovary	772.1 nTPM
Thymus	661.6 nTPM
Skeletal muscle	620.3 nTPM
Lung	594.9 nTPM
Skin	588.6 nTPM
Endometrium	517.6 nTPM
Tongue	505.3 nTPM
Vascular	470.5 nTPM
Prostate	388.6 nTPM
Adipose tissue	326.5 nTPM
Salivary gland	191.1 nTPM
Placenta	188.7 nTPM

Suprabasal keratinocytes	153.5 nTPM
Tongue	184.1 nTPM
Skin	122.9 nTPM

T-cells	76.5 nTPM
Skin	198.7 nTPM
Endometrium	198.1 nTPM
Breast	180.1 nTPM
Colon	177.4 nTPM
Lymph node	151.3 nTPM
Esophagus	124.1 nTPM
Prostate	121.7 nTPM
Tongue	68.6 nTPM
Kidney	49.7 nTPM
Stomach	42.2 nTPM
Spleen	41.2 nTPM
Fallopian tube	39.2 nTPM
Skeletal muscle	33.6 nTPM
PBMC	32.2 nTPM
Thymus	30.3 nTPM
Adipose tissue	27.2 nTPM
Lung	24.5 nTPM
Vascular	21.7 nTPM
Liver	18.4 nTPM
Salivary gland	17.0 nTPM
Bone marrow	10.5 nTPM

Undifferentiated cells	316.1 nTPM
Colon	624.1 nTPM
Small intestine	203.3 nTPM
Rectum	120.9 nTPM

Amygdala excitatory	0.1 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM
Hypothalamus	0.0 nTPM
Thalamus	0.0 nTPM

Astrocyte	227.3 nTPM
Medulla oblongata	470.7 nTPM
Spinal cord	396.3 nTPM
Hypothalamus	315.1 nTPM
Pons	252.7 nTPM
Thalamus	205.4 nTPM
Basal ganglia	195.0 nTPM
Hippocampus	193.9 nTPM
Midbrain	181.7 nTPM
Cerebral cortex	119.0 nTPM
Cerebellum	109.2 nTPM
Amygdala	60.8 nTPM

Bergmann glia	4.6 nTPM
Medulla oblongata	12.8 nTPM
Cerebellum	0.9 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	3.3 nTPM
Medulla oblongata	8.3 nTPM
Spinal cord	7.1 nTPM
Hypothalamus	5.1 nTPM
Hippocampus	3.9 nTPM
Basal ganglia	3.7 nTPM
Cerebellum	2.0 nTPM
Midbrain	1.7 nTPM
Pons	1.6 nTPM
Cerebral cortex	1.5 nTPM
Thalamus	1.3 nTPM
Amygdala	0.4 nTPM

Cerebellar inhibitory	0.3 nTPM
Medulla oblongata	0.9 nTPM
Pons	0.5 nTPM
Cerebellum	0.2 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	1.1 nTPM
Midbrain	3.9 nTPM
Hippocampus	1.2 nTPM
Basal ganglia	0.6 nTPM
Thalamus	0.6 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.4 nTPM
Cerebral cortex	0.3 nTPM

Choroid plexus epithelial cell	25.2 nTPM
Medulla oblongata	69.0 nTPM
Thalamus	16.4 nTPM
Basal ganglia	9.7 nTPM
Hippocampus	5.5 nTPM

Committed oligodendrocyte precursor	10.6 nTPM
Medulla oblongata	25.8 nTPM
Spinal cord	22.1 nTPM
Cerebellum	19.0 nTPM
Pons	18.6 nTPM
Basal ganglia	11.0 nTPM
Thalamus	6.1 nTPM
Hippocampus	5.4 nTPM
Midbrain	4.2 nTPM
Amygdala	2.8 nTPM
Hypothalamus	1.4 nTPM
Cerebral cortex	0.6 nTPM

Deep-layer corticothalamic and 6b	0.1 nTPM
Basal ganglia	0.3 nTPM
Amygdala	0.2 nTPM
Hippocampus	0.2 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	0.2 nTPM
Basal ganglia	0.5 nTPM
Amygdala	0.3 nTPM
Hippocampus	0.2 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.0 nTPM

Deep-layer near-projecting	0.2 nTPM
Hippocampus	0.7 nTPM
Basal ganglia	0.2 nTPM
Amygdala	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hypothalamus	0.0 nTPM

Eccentric medium spiny neuron	0.1 nTPM
Amygdala	0.2 nTPM
Thalamus	0.2 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hypothalamus	0.1 nTPM
Hippocampus	0.0 nTPM