Single cell type - PHF23 - 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.	PHF23
Gene descriptionⁱ Full gene name according to HGNC.	PHD finger protein 23
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes
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.	11

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	Keratinocytes - Keratinization (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

PHF23 is part of cluster 28 Keratinocytes - Keratinization with confidenceⁱ 1
89 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
NXT1	Nuclear transport factor 2 like export factor 1	0.5604	28
YWHAG	Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma	0.5433	28
YTHDF2	YTH N6-methyladenosine RNA binding protein 2	0.5413	10
MARS2	Methionyl-tRNA synthetase 2, mitochondrial	0.5070	28
ERF	ETS2 repressor factor	0.4902	35
CALML5	Calmodulin like 5	0.4866	28
CHIC2	Cysteine rich hydrophobic domain 2	0.4846	28
CLEC2A	C-type lectin domain family 2 member A	0.4727	28
KRT14	Keratin 14	0.4630	28
C1orf109	Chromosome 1 open reading frame 109	0.4589	6
TMEM39B	Transmembrane protein 39B	0.4538	10
HES7	Hes family bHLH transcription factor 7	0.4504	48
PYURF	PIGY upstream reading frame	0.4498	32
CCDC85B	Coiled-coil domain containing 85B	0.4494	51
NAB2	NGFI-A binding protein 2	0.4492	48

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	22.3 nTPM
Adipose tissue	25.6 nTPM
Breast	19.1 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	9.2 nTPM
Lung	9.2 nTPM

Astrocytes	2.0 nTPM
Brain	2.0 nTPM

B-cells	21.9 nTPM
Lymph node	39.0 nTPM
Breast	34.7 nTPM
Colon	27.1 nTPM
PBMC	22.8 nTPM
Adipose tissue	22.5 nTPM
Spleen	22.5 nTPM
Liver	17.7 nTPM
Bone marrow	15.5 nTPM
Stomach	11.8 nTPM
Kidney	4.8 nTPM

Dendritic cells	31.2 nTPM
PBMC	43.8 nTPM
Breast	33.9 nTPM
Adipose tissue	16.0 nTPM

Endothelial cells	26.0 nTPM
Skin	49.6 nTPM
Pancreas	42.5 nTPM
Placenta	32.4 nTPM
Esophagus	31.5 nTPM
Prostate	30.5 nTPM
Endometrium	30.5 nTPM
Testis	27.2 nTPM
Lung	24.9 nTPM
Ovary	22.5 nTPM
Breast	22.5 nTPM
Skeletal muscle	15.3 nTPM
Heart muscle	14.0 nTPM
Liver	12.8 nTPM
Eye	8.1 nTPM

Fibroblasts	20.0 nTPM
Skin	59.8 nTPM
Placenta	31.8 nTPM
Prostate	29.7 nTPM
Ovary	21.0 nTPM
Breast	15.5 nTPM
Stomach	14.9 nTPM
Esophagus	12.8 nTPM
Skeletal muscle	12.7 nTPM
Lung	11.1 nTPM
Adipose tissue	7.1 nTPM
Heart muscle	3.6 nTPM

Intestinal goblet cells	18.5 nTPM
Colon	25.0 nTPM
Rectum	19.1 nTPM
Small intestine	11.3 nTPM

Macrophages	20.8 nTPM
Pancreas	43.4 nTPM
Esophagus	31.5 nTPM
Ovary	30.2 nTPM
PBMC	27.3 nTPM
Kidney	24.9 nTPM
Adipose tissue	23.3 nTPM
Breast	23.3 nTPM
Prostate	21.8 nTPM
Bone marrow	18.8 nTPM
Endometrium	15.7 nTPM
Testis	13.4 nTPM
Spleen	11.4 nTPM
Lung	10.6 nTPM
Skeletal muscle	10.4 nTPM
Stomach	5.9 nTPM

Paneth cells	26.0 nTPM
Small intestine	30.0 nTPM
Colon	29.6 nTPM
Rectum	18.3 nTPM

Plasma cells	23.7 nTPM
Esophagus	67.8 nTPM
Bone marrow	16.5 nTPM
Spleen	14.9 nTPM
Adipose tissue	12.2 nTPM
Stomach	6.8 nTPM

Respiratory ciliated cells	11.4 nTPM
Bronchus	15.5 nTPM
Lung	7.3 nTPM

Smooth muscle cells	29.1 nTPM
Pancreas	61.4 nTPM
Bronchus	52.9 nTPM
Skin	44.0 nTPM
Ovary	37.2 nTPM
Endometrium	27.0 nTPM
Esophagus	20.1 nTPM
Adipose tissue	19.9 nTPM
Breast	17.7 nTPM
Prostate	15.9 nTPM
Heart muscle	14.1 nTPM
Skeletal muscle	9.9 nTPM

T-cells	21.3 nTPM
Skin	38.7 nTPM
Lymph node	33.0 nTPM
Liver	30.9 nTPM
Breast	28.4 nTPM
Esophagus	26.2 nTPM
PBMC	25.9 nTPM
Kidney	25.3 nTPM
Ovary	24.5 nTPM
Adipose tissue	23.8 nTPM
Bone marrow	18.8 nTPM
Skeletal muscle	18.5 nTPM
Spleen	16.7 nTPM
Endometrium	15.6 nTPM
Prostate	9.5 nTPM
Lung	9.1 nTPM
Stomach	9.1 nTPM
Colon	9.0 nTPM

Basal keratinocytes	84.1 nTPM
Skin	84.1 nTPM

Basal prostatic cells	22.7 nTPM
Prostate	22.7 nTPM

Basal respiratory cells	21.6 nTPM
Bronchus	21.6 nTPM

Basal squamous epithelial cells	56.9 nTPM
Esophagus	56.9 nTPM

Undifferentiated cells	16.5 nTPM
Colon	20.7 nTPM
Rectum	17.3 nTPM
Small intestine	11.6 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