Single cell type - IST1 - The Human Protein Atlas

IST1

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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.	IST1
Gene descriptionⁱ Full gene name according to HGNC.	IST1 factor associated with ESCRT-III
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.	18

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.	Monocytes - Innate immune response (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.	Low cell type specificity
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.	0.19
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: Low cell type specificity

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

IST1 is part of cluster 29 Monocytes - Innate immune response with confidenceⁱ 0.94
447 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.
BIRC2	Baculoviral IAP repeat containing 2	0.5649	78
PPP2CA	Protein phosphatase 2 catalytic subunit alpha	0.5635	29
WTAP	WT1 associated protein	0.5528	29
TDG	Thymine DNA glycosylase	0.5140	39
ZCCHC10	Zinc finger CCHC-type containing 10	0.5113	5
CNOT9	CCR4-NOT transcription complex subunit 9	0.4981	29
SHOC2	SHOC2 leucine rich repeat scaffold protein	0.4944	78
PAFAH1B2	Platelet activating factor acetylhydrolase 1b catalytic subunit 2	0.4918	28
PATL1	PAT1 homolog 1, processing body mRNA decay factor	0.4872	37
PAN3	Poly(A) specific ribonuclease subunit PAN3	0.4849	29
HNRNPH1	Heterogeneous nuclear ribonucleoprotein H1	0.4794	80
TAF13	TATA-box binding protein associated factor 13	0.4744	29
NFYA	Nuclear transcription factor Y subunit alpha	0.4735	63
FAM133B	Family with sequence similarity 133 member B	0.4729	78
KDM7A	Lysine demethylase 7A	0.4649	29

IMMUNE CELLS

IST1 is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.96
504 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.
NRBP1	Nuclear receptor binding protein 1	0.9524	35
KCNE1	Potassium voltage-gated channel subfamily E regulatory subunit 1	0.9524	35
FAM177A1	Family with sequence similarity 177 member A1	0.9524	35
ANXA7	Annexin A7	0.9524	35
GMFG	Glia maturation factor gamma	0.9524	35
GDE1	Glycerophosphodiester phosphodiesterase 1	0.9524	35
CSNK1A1	Casein kinase 1 alpha 1	0.9524	42
IK	IK cytokine	0.9286	35
TMCO6	Transmembrane and coiled-coil domains 6	0.9286	35
HBP1	HMG-box transcription factor 1	0.9286	35
SUMO1	Small ubiquitin like modifier 1	0.9286	42
BECN1	Beclin 1	0.9286	42
NUP50	Nucleoporin 50	0.9286	35
ABI1	Abl interactor 1	0.9286	42
BRAP	BRCA1 associated protein	0.9286	35

Adipocytes	57.1 nTPM
Adipose tissue	64.3 nTPM
Breast	50.0 nTPM

Alveolar cells type 1	37.8 nTPM
Lung	37.8 nTPM

Alveolar cells type 2	26.7 nTPM
Lung	26.7 nTPM

Astrocytes	37.8 nTPM
Brain	37.8 nTPM

B-cells	53.1 nTPM
Adipose tissue	82.3 nTPM
Lymph node	73.0 nTPM
Stomach	61.2 nTPM
Spleen	60.1 nTPM
Esophagus	59.0 nTPM
Skin	50.8 nTPM
Bone marrow	50.2 nTPM
Salivary gland	48.6 nTPM
Thymus	47.8 nTPM
PBMC	46.2 nTPM
Lung	40.2 nTPM
Kidney	36.4 nTPM
Liver	33.8 nTPM

Ciliated cells	41.4 nTPM
Bronchus	56.2 nTPM
Endometrium	49.8 nTPM
Fallopian tube	33.9 nTPM
Lung	25.6 nTPM

Club cells	40.9 nTPM
Bronchus	50.2 nTPM
Prostate	46.3 nTPM
Lung	26.2 nTPM

Dendritic cells	70.2 nTPM
Adipose tissue	90.1 nTPM
PBMC	50.4 nTPM

Endothelial cells	48.9 nTPM
Liver	66.8 nTPM
Skin	63.1 nTPM
Pancreas	59.5 nTPM
Endometrium	52.8 nTPM
Fallopian tube	52.8 nTPM
Breast	51.0 nTPM
Skeletal muscle	50.6 nTPM
Testis	50.4 nTPM
Ovary	49.9 nTPM
Vascular	46.2 nTPM
Heart muscle	44.5 nTPM
Lung	44.2 nTPM
Placenta	43.7 nTPM
Thymus	42.3 nTPM
Salivary gland	41.2 nTPM
Prostate	40.7 nTPM
Esophagus	40.2 nTPM
Tongue	40.2 nTPM

Enteroendocrine cells	61.5 nTPM
Small intestine	72.1 nTPM
Rectum	58.7 nTPM
Colon	53.7 nTPM

Fibroblasts	40.5 nTPM
Skin	72.8 nTPM
Placenta	57.4 nTPM
Fallopian tube	48.6 nTPM
Liver	46.3 nTPM
Breast	43.9 nTPM
Adipose tissue	42.8 nTPM
Vascular	38.5 nTPM
Prostate	38.3 nTPM
Salivary gland	37.5 nTPM
Skeletal muscle	37.3 nTPM
Esophagus	35.9 nTPM
Heart muscle	35.1 nTPM
Pancreas	34.5 nTPM
Thymus	30.5 nTPM
Lung	29.2 nTPM
Stomach	20.2 nTPM

Granulocytes	59.3 nTPM
Fallopian tube	80.5 nTPM
Tongue	58.2 nTPM
Lung	39.3 nTPM

Intestinal goblet cells	77.1 nTPM
Small intestine	95.0 nTPM
Rectum	77.1 nTPM
Colon	59.1 nTPM

Lymphatic endothelial cells	43.2 nTPM
Fallopian tube	53.7 nTPM
Ovary	32.7 nTPM

Macrophages	59.9 nTPM
Adipose tissue	111.0 nTPM
Fallopian tube	105.3 nTPM
Skin	85.8 nTPM
Spleen	70.2 nTPM
Kidney	60.2 nTPM
Pancreas	55.5 nTPM
Vascular	55.3 nTPM
Lung	53.8 nTPM
Salivary gland	53.7 nTPM
Endometrium	53.5 nTPM
Tongue	51.9 nTPM
Bone marrow	51.7 nTPM
Thymus	51.7 nTPM
Stomach	51.4 nTPM
Testis	49.6 nTPM
Esophagus	48.8 nTPM
Prostate	44.1 nTPM
Skeletal muscle	42.7 nTPM
Breast	41.4 nTPM

Basal keratinocytes	66.0 nTPM
Skin	97.2 nTPM
Tongue	34.8 nTPM

Basal prostatic cells	41.5 nTPM
Prostate	41.5 nTPM

Basal squamous epithelial cells	33.7 nTPM
Esophagus	33.7 nTPM

Bipolar cells	23.6 nTPM
Eye	23.6 nTPM

Paneth cells	69.3 nTPM
Colon	83.2 nTPM
Small intestine	65.6 nTPM
Rectum	59.0 nTPM

Plasma cells	35.4 nTPM
Fallopian tube	47.3 nTPM
Esophagus	41.6 nTPM
Liver	39.6 nTPM
Salivary gland	36.3 nTPM
Stomach	35.6 nTPM
Spleen	29.8 nTPM
Thymus	28.9 nTPM
Bone marrow	24.2 nTPM

Schwann cells	36.5 nTPM
Adipose tissue	71.8 nTPM
Vascular	25.6 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	36.5 nTPM
Salivary gland	37.6 nTPM
Tongue	35.4 nTPM

Smooth muscle cells	43.1 nTPM
Skin	75.7 nTPM
Liver	59.9 nTPM
Placenta	47.2 nTPM
Endometrium	45.4 nTPM
Adipose tissue	45.2 nTPM
Prostate	44.4 nTPM
Fallopian tube	41.1 nTPM
Vascular	40.6 nTPM
Breast	39.6 nTPM
Tongue	38.3 nTPM
Esophagus	37.2 nTPM
Salivary gland	36.6 nTPM
Ovary	36.3 nTPM
Lung	35.3 nTPM
Skeletal muscle	34.2 nTPM
Thymus	32.9 nTPM

Suprabasal keratinocytes	65.4 nTPM
Skin	91.3 nTPM
Tongue	39.4 nTPM

T-cells	50.4 nTPM
Adipose tissue	90.8 nTPM
Fallopian tube	74.9 nTPM
Skin	65.5 nTPM
Endometrium	58.9 nTPM
Colon	56.5 nTPM
Breast	53.2 nTPM
Prostate	51.6 nTPM
Spleen	51.5 nTPM
Liver	49.6 nTPM
Lymph node	49.6 nTPM
Tongue	49.3 nTPM
Stomach	49.0 nTPM
Vascular	46.2 nTPM
Bone marrow	44.8 nTPM
PBMC	44.0 nTPM
Thymus	43.3 nTPM
Salivary gland	40.7 nTPM
Kidney	39.0 nTPM
Skeletal muscle	35.9 nTPM
Esophagus	31.6 nTPM
Lung	31.5 nTPM

Undifferentiated cells	45.4 nTPM
Small intestine	51.3 nTPM
Rectum	50.1 nTPM
Colon	34.7 nTPM

Amygdala excitatory	54.6 nTPM
Thalamus	63.1 nTPM
Hypothalamus	60.9 nTPM
Amygdala	51.4 nTPM
Basal ganglia	50.9 nTPM
Hippocampus	50.7 nTPM
Cerebral cortex	50.6 nTPM

Astrocyte	68.0 nTPM
Spinal cord	76.8 nTPM
Cerebellum	73.0 nTPM
Pons	73.0 nTPM
Midbrain	70.5 nTPM
Thalamus	70.5 nTPM
Basal ganglia	68.2 nTPM
Cerebral cortex	66.0 nTPM
Hippocampus	65.6 nTPM
Amygdala	64.8 nTPM
Medulla oblongata	63.3 nTPM
Hypothalamus	56.5 nTPM

Bergmann glia	55.5 nTPM
Medulla oblongata	63.9 nTPM
Cerebellum	58.0 nTPM
Pons	44.6 nTPM

Central nervous system macrophage	111.0 nTPM
Amygdala	134.8 nTPM
Hippocampus	126.6 nTPM
Cerebral cortex	116.3 nTPM
Basal ganglia	113.0 nTPM
Thalamus	111.7 nTPM
Midbrain	110.7 nTPM
Pons	109.3 nTPM
Hypothalamus	105.6 nTPM
Spinal cord	102.7 nTPM
Cerebellum	98.6 nTPM
Medulla oblongata	91.5 nTPM

Cerebellar inhibitory	60.1 nTPM
Spinal cord	74.2 nTPM
Medulla oblongata	60.6 nTPM
Cerebellum	58.5 nTPM
Pons	56.5 nTPM
Midbrain	50.7 nTPM

Cge interneuron	52.5 nTPM
Hypothalamus	65.8 nTPM
Amygdala	55.3 nTPM
Thalamus	52.5 nTPM
Cerebral cortex	49.6 nTPM
Basal ganglia	48.8 nTPM
Hippocampus	48.7 nTPM
Midbrain	46.7 nTPM

Choroid plexus epithelial cell	69.0 nTPM
Basal ganglia	97.1 nTPM
Medulla oblongata	71.3 nTPM
Hippocampus	61.0 nTPM
Thalamus	46.6 nTPM

Committed oligodendrocyte precursor	72.3 nTPM
Hypothalamus	86.7 nTPM
Thalamus	79.2 nTPM
Midbrain	74.8 nTPM
Hippocampus	73.0 nTPM
Pons	72.6 nTPM
Amygdala	71.6 nTPM
Cerebral cortex	71.6 nTPM
Cerebellum	68.2 nTPM
Spinal cord	66.2 nTPM
Medulla oblongata	65.8 nTPM
Basal ganglia	65.7 nTPM

Deep-layer corticothalamic and 6b	53.2 nTPM
Hypothalamus	63.9 nTPM
Midbrain	59.9 nTPM
Amygdala	52.0 nTPM
Hippocampus	48.3 nTPM
Basal ganglia	47.7 nTPM
Cerebral cortex	47.6 nTPM

Deep-layer intratelencephalic	52.1 nTPM
Hypothalamus	62.4 nTPM
Amygdala	54.2 nTPM
Cerebral cortex	49.3 nTPM
Basal ganglia	47.6 nTPM
Hippocampus	47.0 nTPM

Deep-layer near-projecting	64.4 nTPM
Hypothalamus	80.3 nTPM
Amygdala	73.0 nTPM
Cerebral cortex	65.2 nTPM
Basal ganglia	53.6 nTPM
Hippocampus	50.1 nTPM

Eccentric medium spiny neuron	51.4 nTPM
Thalamus	52.9 nTPM
Amygdala	52.2 nTPM
Hypothalamus	51.9 nTPM
Cerebral cortex	51.5 nTPM
Hippocampus	50.6 nTPM
Basal ganglia	49.1 nTPM