Single cell type - FOXA1 - The Human Protein Atlas

FOXA1

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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.	FOXA1
Gene descriptionⁱ Full gene name according to HGNC.	Forkhead box A1
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.	Prostatic glandular cells - 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 (Prostatic glandular cells, Breast glandular cells, Enteroendocrine cells, Club cells, Basal squamous epithelial 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.	0.76
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 enriched (Ependymal cell)
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 (Prostatic glandular cells, Breast glandular cells, Enteroendocrine cells, Club cells, Basal squamous epithelial 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 enriched (Ependymal cell)

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

FOXA1 is part of cluster 40 Prostatic glandular cells - Transcription with confidenceⁱ 1
76 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.
MSMB	Microseminoprotein beta	0.7691	40
CREB3L4	CAMP responsive element binding protein 3 like 4	0.7337	40
MESP1	Mesoderm posterior bHLH transcription factor 1	0.7265	40
ARHGEF38	Rho guanine nucleotide exchange factor 38	0.7151	40
ACP3	Acid phosphatase 3	0.6894	40
ARHGAP40	Rho GTPase activating protein 40	0.6803	17
KLK2	Kallikrein related peptidase 2	0.6771	40
KLK3	Kallikrein related peptidase 3	0.6766	40
TGM4	Transglutaminase 4	0.6729	40
POTEM	POTE ankyrin domain family member M	0.6708	40
POTEH	POTE ankyrin domain family member H	0.6671	40
STEAP2	STEAP2 metalloreductase	0.6576	40
NPY	Neuropeptide Y	0.6548	40
NKX3-1	NK3 homeobox 1	0.6476	40
NEFH	Neurofilament heavy chain	0.6459	40

Adipocytes	0.7 nTPM
Breast	1.3 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	24.3 nTPM
Lung	24.3 nTPM

Alveolar cells type 2	34.9 nTPM
Lung	34.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.0 nTPM
Salivary gland	0.1 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	40.9 nTPM
Lung	86.4 nTPM
Bronchus	69.3 nTPM
Fallopian tube	5.0 nTPM
Endometrium	2.9 nTPM

Club cells	76.8 nTPM
Prostate	97.2 nTPM
Lung	74.7 nTPM
Bronchus	58.5 nTPM

Endothelial cells	0.9 nTPM
Tongue	7.8 nTPM
Liver	2.5 nTPM
Lung	2.1 nTPM
Salivary gland	2.0 nTPM
Esophagus	0.8 nTPM
Endometrium	0.5 nTPM
Prostate	0.5 nTPM
Testis	0.3 nTPM
Heart muscle	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	77.2 nTPM
Rectum	122.4 nTPM
Small intestine	75.5 nTPM
Colon	33.5 nTPM

Fibroblasts	0.4 nTPM
Prostate	1.3 nTPM
Salivary gland	1.3 nTPM
Liver	1.2 nTPM
Breast	1.2 nTPM
Lung	0.6 nTPM
Esophagus	0.3 nTPM
Pancreas	0.2 nTPM
Fallopian tube	0.2 nTPM
Skin	0.1 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Heart muscle	0.0 nTPM
Placenta	0.0 nTPM
Skeletal muscle	0.0 nTPM
Stomach	0.0 nTPM
Vascular	0.0 nTPM

Granulocytes	0.6 nTPM
Lung	1.5 nTPM
Fallopian tube	0.2 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	36.8 nTPM
Rectum	54.5 nTPM
Colon	37.2 nTPM
Small intestine	18.9 nTPM

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

Macrophages	0.9 nTPM
Tongue	7.2 nTPM
Prostate	2.1 nTPM
Breast	1.8 nTPM
Salivary gland	1.4 nTPM
Skin	1.1 nTPM
Endometrium	0.6 nTPM
Vascular	0.6 nTPM
Fallopian tube	0.5 nTPM
Adipose tissue	0.4 nTPM
Lung	0.4 nTPM
Skeletal muscle	0.2 nTPM
Testis	0.0 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM

Paneth cells	34.8 nTPM
Rectum	51.2 nTPM
Colon	28.9 nTPM
Small intestine	24.2 nTPM

Cholangiocytes	34.3 nTPM
Liver	34.3 nTPM

Collecting duct cells	3.9 nTPM
Kidney	3.9 nTPM

Distal enterocytes	34.2 nTPM
Rectum	38.0 nTPM
Colon	30.5 nTPM

Plasma cells	1.5 nTPM
Salivary gland	5.4 nTPM
Esophagus	5.2 nTPM
Liver	1.5 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Thymus	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.3 nTPM
Adipose tissue	0.8 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	24.4 nTPM
Tongue	48.6 nTPM
Salivary gland	0.2 nTPM

Smooth muscle cells	0.4 nTPM
Tongue	1.8 nTPM
Lung	1.2 nTPM
Breast	1.0 nTPM
Liver	0.8 nTPM
Prostate	0.6 nTPM
Endometrium	0.2 nTPM
Adipose tissue	0.2 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.6 nTPM
Tongue	3.8 nTPM
Esophagus	2.4 nTPM
Salivary gland	1.7 nTPM
Endometrium	1.3 nTPM
Liver	1.2 nTPM
Breast	0.8 nTPM
Prostate	0.7 nTPM
Lung	0.5 nTPM
Fallopian tube	0.3 nTPM
Stomach	0.2 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	29.7 nTPM
Rectum	45.1 nTPM
Colon	29.6 nTPM
Small intestine	14.4 nTPM

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

Astrocyte	0.1 nTPM
Midbrain	0.4 nTPM
Thalamus	0.4 nTPM
Medulla oblongata	0.2 nTPM
Pons	0.2 nTPM
Hypothalamus	0.1 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Spinal cord	0.0 nTPM

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

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

Cerebellar inhibitory	0.0 nTPM
Pons	0.1 nTPM
Cerebellum	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM

Cge interneuron	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Midbrain	0.0 nTPM
Thalamus	0.0 nTPM

Choroid plexus epithelial cell	0.7 nTPM
Thalamus	2.7 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Medulla oblongata	0.0 nTPM

Committed oligodendrocyte precursor	0.0 nTPM
Thalamus	0.2 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM

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

Deep-layer intratelencephalic	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM

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

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

Endothelial cell	0.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Medulla oblongata	0.0 nTPM
Midbrain	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Ependymal cell	6.8 nTPM
Spinal cord	19.2 nTPM
Thalamus	10.5 nTPM
Midbrain	10.2 nTPM
Hypothalamus	9.8 nTPM
Medulla oblongata	4.2 nTPM
Hippocampus	2.9 nTPM
Pons	2.4 nTPM
Amygdala	1.7 nTPM
Basal ganglia	0.5 nTPM