Single cell type - CFTR - The Human Protein Atlas

CFTR

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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.	CFTR
Gene descriptionⁱ Full gene name according to HGNC.	CF transmembrane conductance regulator
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Enzymes FDA approved drug targets Human disease related genes Plasma proteins Transporters
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	14

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.	Non-specific - 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.	Group enriched (Ductal cells, Late spermatids)
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.	0.81
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 (Oligodendrocyte)
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: Group enriched (Ductal cells, Late spermatids)

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 (Oligodendrocyte)

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

CFTR is part of cluster 45 Non-specific - Mixed function with confidenceⁱ 1
349 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.
HTR3A	5-hydroxytryptamine receptor 3A	0.7404	45
NEURL3	Neuralized E3 ubiquitin protein ligase 3	0.7337	45
SCTR	Secretin receptor	0.7300	45
DUOXA2	Dual oxidase maturation factor 2	0.7130	45
CUZD1	CUB and zona pellucida like domains 1	0.6993	45
KRTAP1-1	Keratin associated protein 1-1	0.6913	45
REG1B	Regenerating family member 1 beta	0.6897	45
REG1A	Regenerating family member 1 alpha	0.6740	45
UBD	Ubiquitin D	0.6682	45
CTRB2	Chymotrypsinogen B2	0.6674	45
PDX1	Pancreatic and duodenal homeobox 1	0.6493	45
MMP7	Matrix metallopeptidase 7	0.6451	45
PGA5	Pepsinogen A5	0.6410	45
NCMAP	Non-compact myelin associated protein	0.6241	45
SPINK1	Serine peptidase inhibitor Kazal type 1	0.6109	45

Adipocytes	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	0.0 nTPM

Alveolar cells type 1	2.2 nTPM
Lung	2.2 nTPM

Alveolar cells type 2	37.9 nTPM
Lung	37.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.1 nTPM
Salivary gland	1.3 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	3.5 nTPM
Endometrium	6.6 nTPM
Lung	4.0 nTPM
Fallopian tube	2.3 nTPM
Bronchus	1.0 nTPM

Club cells	19.5 nTPM
Lung	27.6 nTPM
Prostate	19.6 nTPM
Bronchus	11.4 nTPM

Endothelial cells	5.1 nTPM
Pancreas	87.9 nTPM
Salivary gland	2.6 nTPM
Lung	0.9 nTPM
Endometrium	0.3 nTPM
Prostate	0.2 nTPM
Thymus	0.1 nTPM
Tongue	0.1 nTPM
Vascular	0.1 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.1 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Breast	0.0 nTPM

Enteroendocrine cells	37.4 nTPM
Colon	93.7 nTPM
Rectum	11.7 nTPM
Small intestine	6.9 nTPM

Fibroblasts	1.5 nTPM
Pancreas	20.9 nTPM
Salivary gland	2.1 nTPM
Lung	0.9 nTPM
Breast	0.2 nTPM
Fallopian tube	0.2 nTPM
Thymus	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM
Vascular	0.0 nTPM

Granulocytes	0.4 nTPM
Lung	1.0 nTPM
Fallopian tube	0.2 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	14.7 nTPM
Rectum	27.7 nTPM
Colon	12.1 nTPM
Small intestine	4.3 nTPM

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.2 nTPM
Salivary gland	3.6 nTPM
Tongue	0.3 nTPM
Skeletal muscle	0.2 nTPM
Lung	0.2 nTPM
Fallopian tube	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM

Paneth cells	81.9 nTPM
Small intestine	196.9 nTPM
Rectum	37.9 nTPM
Colon	10.9 nTPM

Cholangiocytes	64.9 nTPM
Liver	64.9 nTPM

Collecting duct cells	1.9 nTPM
Kidney	1.9 nTPM

Cone photoreceptor cells	1.7 nTPM
Eye	1.7 nTPM

Distal enterocytes	76.6 nTPM
Rectum	100.7 nTPM
Colon	52.3 nTPM

Plasma cells	0.5 nTPM
Salivary gland	3.6 nTPM
Fallopian tube	0.3 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM

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

Serous glandular cells	9.2 nTPM
Salivary gland	9.5 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	0.2 nTPM
Salivary gland	2.6 nTPM
Endometrium	0.6 nTPM
Tongue	0.3 nTPM
Fallopian tube	0.2 nTPM
Placenta	0.1 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.3 nTPM
Colon	1.9 nTPM
Endometrium	1.1 nTPM
Vascular	0.8 nTPM
Salivary gland	0.6 nTPM
Lung	0.5 nTPM
Stomach	0.1 nTPM
Tongue	0.1 nTPM
Fallopian tube	0.1 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Prostate	0.0 nTPM
Thymus	0.0 nTPM
Breast	0.0 nTPM

Undifferentiated cells	53.5 nTPM
Rectum	77.1 nTPM
Colon	43.4 nTPM
Small intestine	40.0 nTPM

Amygdala excitatory	12.7 nTPM
Cerebral cortex	15.7 nTPM
Hippocampus	15.6 nTPM
Thalamus	15.4 nTPM
Amygdala	14.3 nTPM
Basal ganglia	10.9 nTPM
Hypothalamus	4.3 nTPM

Astrocyte	8.7 nTPM
Spinal cord	21.7 nTPM
Medulla oblongata	14.6 nTPM
Pons	12.9 nTPM
Hypothalamus	9.8 nTPM
Basal ganglia	9.0 nTPM
Midbrain	8.1 nTPM
Thalamus	6.1 nTPM
Cerebellum	3.6 nTPM
Amygdala	3.5 nTPM
Hippocampus	3.5 nTPM
Cerebral cortex	3.2 nTPM

Bergmann glia	0.5 nTPM
Cerebellum	1.6 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	28.2 nTPM
Basal ganglia	44.8 nTPM
Spinal cord	41.8 nTPM
Medulla oblongata	32.1 nTPM
Thalamus	28.3 nTPM
Pons	27.9 nTPM
Hypothalamus	27.3 nTPM
Cerebellum	24.3 nTPM
Cerebral cortex	24.3 nTPM
Midbrain	22.2 nTPM
Hippocampus	20.8 nTPM
Amygdala	16.0 nTPM

Cerebellar inhibitory	16.9 nTPM
Pons	27.2 nTPM
Medulla oblongata	21.9 nTPM
Midbrain	17.4 nTPM
Cerebellum	9.6 nTPM
Spinal cord	8.2 nTPM

Cge interneuron	13.7 nTPM
Hippocampus	18.3 nTPM
Midbrain	16.3 nTPM
Cerebral cortex	15.2 nTPM
Basal ganglia	14.5 nTPM
Amygdala	13.6 nTPM
Thalamus	13.6 nTPM
Hypothalamus	4.4 nTPM

Choroid plexus epithelial cell	9.1 nTPM
Thalamus	13.7 nTPM
Hippocampus	11.1 nTPM
Medulla oblongata	9.6 nTPM
Basal ganglia	2.1 nTPM

Committed oligodendrocyte precursor	97.9 nTPM
Spinal cord	169.2 nTPM
Cerebellum	109.4 nTPM
Pons	108.0 nTPM
Midbrain	101.6 nTPM
Medulla oblongata	94.2 nTPM
Cerebral cortex	89.3 nTPM
Hippocampus	85.9 nTPM
Thalamus	85.8 nTPM
Amygdala	79.5 nTPM
Basal ganglia	77.2 nTPM
Hypothalamus	77.2 nTPM

Deep-layer corticothalamic and 6b	20.4 nTPM
Hippocampus	27.1 nTPM
Cerebral cortex	26.7 nTPM
Basal ganglia	21.5 nTPM
Midbrain	20.0 nTPM
Amygdala	19.3 nTPM
Hypothalamus	7.9 nTPM

Deep-layer intratelencephalic	13.5 nTPM
Hippocampus	18.1 nTPM
Basal ganglia	17.1 nTPM
Amygdala	16.4 nTPM
Cerebral cortex	13.0 nTPM
Hypothalamus	2.8 nTPM

Deep-layer near-projecting	16.0 nTPM
Hippocampus	28.6 nTPM
Cerebral cortex	18.4 nTPM
Basal ganglia	17.5 nTPM
Amygdala	12.0 nTPM
Hypothalamus	3.6 nTPM

Eccentric medium spiny neuron	31.5 nTPM
Basal ganglia	39.4 nTPM
Hippocampus	36.5 nTPM
Thalamus	36.0 nTPM
Amygdala	28.3 nTPM
Cerebral cortex	27.3 nTPM
Hypothalamus	21.3 nTPM

Endothelial cell	15.7 nTPM
Basal ganglia	29.8 nTPM
Hypothalamus	29.8 nTPM
Hippocampus	16.7 nTPM
Midbrain	16.1 nTPM
Thalamus	15.2 nTPM
Cerebellum	14.7 nTPM
Cerebral cortex	12.8 nTPM
Amygdala	12.3 nTPM
Medulla oblongata	11.3 nTPM
Pons	8.7 nTPM
Spinal cord	5.2 nTPM

Ependymal cell	62.6 nTPM
Spinal cord	461.9 nTPM
Medulla oblongata	45.0 nTPM
Pons	18.9 nTPM
Hypothalamus	10.7 nTPM
Basal ganglia	8.3 nTPM
Hippocampus	5.9 nTPM
Amygdala	5.7 nTPM
Thalamus	3.6 nTPM
Midbrain	3.2 nTPM