Single cell type - PHAX - The Human Protein Atlas

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.	PHAX
Gene descriptionⁱ Full gene name according to HGNC.	Phosphorylated adaptor for RNA export
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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. Read more	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. Read more	Non-specific - 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. Read more	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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

PHAX is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 0.99
482 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
U2SURP	U2 snRNP associated SURP domain containing	0.6060	10
MED18	Mediator complex subunit 18	0.5691	39
THRAP3	Thyroid hormone receptor associated protein 3	0.5460	10
PUF60	Poly(U) binding splicing factor 60	0.5259	10
SNRNP35	Small nuclear ribonucleoprotein U11/U12 subunit 35	0.5249	26
ZNF256	Zinc finger protein 256	0.5191	52
DNAJC8	DnaJ heat shock protein family (Hsp40) member C8	0.5120	39
THYN1	Thymocyte nuclear protein 1	0.4964	39
LARP7	La ribonucleoprotein 7, transcriptional regulator	0.4941	39
SON	SON DNA and RNA binding protein	0.4921	43
SERF1A	Small EDRK-rich factor 1A	0.4812	43
PRPF6	Pre-mRNA processing factor 6	0.4812	52
GPATCH11	G-patch domain containing 11	0.4809	10
CDC23	Cell division cycle 23	0.4745	18
MFAP1	Microfibril associated protein 1	0.4735	10

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	34.6 nTPM
Breast	44.4 nTPM
Adipose tissue	24.8 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	40.2 nTPM
Lung	40.2 nTPM

Astrocytes	10.7 nTPM
Brain	10.7 nTPM

B-cells	36.1 nTPM
Kidney	71.4 nTPM
Liver	46.1 nTPM
Colon	44.8 nTPM
Adipose tissue	35.1 nTPM
Bone marrow	33.5 nTPM
Breast	30.7 nTPM
PBMC	28.5 nTPM
Stomach	28.2 nTPM
Spleen	25.0 nTPM
Lymph node	17.5 nTPM

Dendritic cells	42.4 nTPM
Adipose tissue	46.2 nTPM
Breast	45.2 nTPM
PBMC	35.8 nTPM

Endothelial cells	36.8 nTPM
Heart muscle	77.5 nTPM
Pancreas	50.2 nTPM
Testis	44.2 nTPM
Skeletal muscle	41.0 nTPM
Lung	40.6 nTPM
Ovary	39.6 nTPM
Eye	37.2 nTPM
Placenta	35.3 nTPM
Endometrium	30.3 nTPM
Breast	29.1 nTPM
Esophagus	23.2 nTPM
Liver	22.9 nTPM
Skin	22.5 nTPM
Prostate	21.0 nTPM

Fibroblasts	41.8 nTPM
Heart muscle	114.7 nTPM
Skeletal muscle	45.7 nTPM
Adipose tissue	40.6 nTPM
Lung	40.2 nTPM
Breast	38.5 nTPM
Ovary	38.4 nTPM
Placenta	37.7 nTPM
Esophagus	29.4 nTPM
Stomach	26.7 nTPM
Skin	26.4 nTPM
Prostate	21.8 nTPM

Intestinal goblet cells	26.9 nTPM
Colon	30.0 nTPM
Small intestine	28.2 nTPM
Rectum	22.5 nTPM

Macrophages	21.9 nTPM
Lung	48.7 nTPM
Pancreas	43.4 nTPM
Ovary	38.3 nTPM
Testis	29.1 nTPM
Kidney	28.7 nTPM
Breast	27.0 nTPM
Endometrium	19.1 nTPM
Adipose tissue	17.5 nTPM
Prostate	17.2 nTPM
Skeletal muscle	16.7 nTPM
Esophagus	15.8 nTPM
Bone marrow	11.3 nTPM
Spleen	9.3 nTPM
Stomach	5.9 nTPM
PBMC	0.0 nTPM

Paneth cells	23.1 nTPM
Small intestine	37.6 nTPM
Rectum	25.1 nTPM
Colon	6.5 nTPM

Plasma cells	29.7 nTPM
Bone marrow	37.9 nTPM
Spleen	37.7 nTPM
Stomach	32.2 nTPM
Adipose tissue	22.5 nTPM
Esophagus	18.4 nTPM

Respiratory ciliated cells	63.3 nTPM
Lung	83.1 nTPM
Bronchus	43.6 nTPM

Smooth muscle cells	51.7 nTPM
Heart muscle	113.7 nTPM
Bronchus	111.7 nTPM
Pancreas	57.2 nTPM
Ovary	56.0 nTPM
Endometrium	42.7 nTPM
Breast	41.3 nTPM
Skeletal muscle	35.3 nTPM
Adipose tissue	32.4 nTPM
Esophagus	29.4 nTPM
Skin	24.7 nTPM
Prostate	24.4 nTPM

T-cells	34.2 nTPM
Lung	56.2 nTPM
Ovary	55.6 nTPM
Kidney	50.0 nTPM
PBMC	50.0 nTPM
Adipose tissue	46.4 nTPM
Endometrium	38.2 nTPM
Breast	37.4 nTPM
Skeletal muscle	37.1 nTPM
Colon	35.1 nTPM
Liver	32.9 nTPM
Bone marrow	31.3 nTPM
Skin	30.4 nTPM
Stomach	30.1 nTPM
Spleen	24.3 nTPM
Lymph node	20.5 nTPM
Esophagus	6.6 nTPM
Prostate	0.0 nTPM

Basal keratinocytes	28.6 nTPM
Skin	28.6 nTPM

Basal prostatic cells	31.6 nTPM
Prostate	31.6 nTPM

Basal respiratory cells	72.1 nTPM
Bronchus	72.1 nTPM

Cholangiocytes	20.0 nTPM
Liver	20.0 nTPM

Undifferentiated cells	27.7 nTPM
Colon	33.6 nTPM
Rectum	25.9 nTPM
Small intestine	23.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC