Single cell type - NPAT - 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.	NPAT
Gene descriptionⁱ Full gene name according to HGNC.	Nuclear protein, coactivator of histone transcription
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.	2

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 - 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. 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	Cell line enhanced (U-698)
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

NPAT is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
METTL4	Methyltransferase like 4	0.7235	59
ZNF235	Zinc finger protein 235	0.6682	59
CEP120	Centrosomal protein 120	0.6614	59
ZNF107	Zinc finger protein 107	0.6575	57
ZNF484	Zinc finger protein 484	0.6511	59
DMRTC1	DMRT like family C1	0.5901	59
WDR89	WD repeat domain 89	0.5770	58
DPH1	Diphthamide biosynthesis 1	0.5764	59
ZNF564	Zinc finger protein 564	0.5750	59
FCMR	Fc fragment of IgM receptor	0.5712	57
ZCCHC4	Zinc finger CCHC-type containing 4	0.5705	59
PARP15	Poly(ADP-ribose) polymerase family member 15	0.5695	57
SP140	SP140 nuclear body protein	0.5633	57
GRAPL	GRB2 related adaptor protein like	0.5546	14
SLC25A32	Solute carrier family 25 member 32	0.5520	59

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	23.1 nTPM
Adipose tissue	24.9 nTPM
Breast	21.4 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	13.2 nTPM
Lung	13.2 nTPM

Astrocytes	24.2 nTPM
Brain	24.2 nTPM

B-cells	40.8 nTPM
Adipose tissue	65.6 nTPM
Colon	60.7 nTPM
Spleen	59.8 nTPM
Lymph node	58.1 nTPM
Stomach	44.0 nTPM
Bone marrow	39.2 nTPM
PBMC	24.3 nTPM
Breast	20.0 nTPM
Kidney	19.0 nTPM
Liver	17.3 nTPM

Dendritic cells	32.8 nTPM
Adipose tissue	54.6 nTPM
Breast	27.7 nTPM
PBMC	16.0 nTPM

Endothelial cells	21.1 nTPM
Lung	37.4 nTPM
Heart muscle	35.2 nTPM
Esophagus	29.3 nTPM
Prostate	24.5 nTPM
Skeletal muscle	23.1 nTPM
Liver	22.0 nTPM
Endometrium	21.5 nTPM
Testis	19.0 nTPM
Skin	19.0 nTPM
Breast	17.7 nTPM
Ovary	16.7 nTPM
Eye	16.2 nTPM
Pancreas	7.7 nTPM
Placenta	5.7 nTPM

Fibroblasts	15.9 nTPM
Prostate	19.2 nTPM
Skeletal muscle	17.1 nTPM
Adipose tissue	17.0 nTPM
Lung	16.8 nTPM
Esophagus	16.8 nTPM
Breast	16.6 nTPM
Heart muscle	16.3 nTPM
Stomach	16.3 nTPM
Skin	14.5 nTPM
Ovary	14.0 nTPM
Placenta	10.2 nTPM

Intestinal goblet cells	7.9 nTPM
Rectum	10.7 nTPM
Small intestine	8.0 nTPM
Colon	5.0 nTPM

Macrophages	13.8 nTPM
Adipose tissue	21.6 nTPM
Lung	21.4 nTPM
Skeletal muscle	21.2 nTPM
Testis	17.4 nTPM
Breast	16.9 nTPM
Ovary	16.4 nTPM
Bone marrow	16.3 nTPM
Prostate	15.0 nTPM
Endometrium	13.7 nTPM
Stomach	11.7 nTPM
Spleen	10.4 nTPM
Esophagus	9.4 nTPM
Pancreas	7.7 nTPM
Kidney	7.6 nTPM
PBMC	0.0 nTPM

Paneth cells	6.5 nTPM
Rectum	8.8 nTPM
Small intestine	7.5 nTPM
Colon	3.3 nTPM

Plasma cells	37.8 nTPM
Adipose tissue	60.7 nTPM
Stomach	37.8 nTPM
Esophagus	36.9 nTPM
Bone marrow	31.3 nTPM
Spleen	22.1 nTPM

Respiratory ciliated cells	10.9 nTPM
Lung	11.7 nTPM
Bronchus	10.1 nTPM

Smooth muscle cells	13.1 nTPM
Heart muscle	18.4 nTPM
Skeletal muscle	18.3 nTPM
Adipose tissue	16.4 nTPM
Endometrium	16.1 nTPM
Prostate	15.9 nTPM
Breast	13.0 nTPM
Esophagus	12.4 nTPM
Ovary	11.3 nTPM
Skin	9.1 nTPM
Bronchus	7.5 nTPM
Pancreas	5.8 nTPM

T-cells	35.3 nTPM
Adipose tissue	58.8 nTPM
Spleen	56.9 nTPM
Lymph node	53.8 nTPM
Bone marrow	53.5 nTPM
Lung	47.1 nTPM
PBMC	42.7 nTPM
Endometrium	34.8 nTPM
Skeletal muscle	32.4 nTPM
Stomach	30.7 nTPM
Breast	30.0 nTPM
Skin	29.5 nTPM
Colon	27.6 nTPM
Kidney	26.7 nTPM
Liver	24.4 nTPM
Ovary	20.1 nTPM
Prostate	19.0 nTPM
Esophagus	13.1 nTPM

Basal respiratory cells	10.5 nTPM
Bronchus	10.5 nTPM

Basal squamous epithelial cells	27.3 nTPM
Esophagus	27.3 nTPM

Cholangiocytes	4.3 nTPM
Liver	4.3 nTPM

Collecting duct cells	12.9 nTPM
Kidney	12.9 nTPM

Undifferentiated cells	8.7 nTPM
Small intestine	10.0 nTPM
Rectum	9.7 nTPM
Colon	6.4 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