Single cell type - JADE1 - 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.	JADE1
Gene descriptionⁱ Full gene name according to HGNC.	Jade family PHD finger 1
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.	13

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	Fibroblasts - ECM organization (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

JADE1 is part of cluster 50 Fibroblasts - ECM organization with confidenceⁱ 1
441 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
DEPP1	DEPP1 autophagy regulator	0.5761	50
PALM2AKAP2	PALM2 and AKAP2 fusion	0.5660	50
AGTR1	Angiotensin II receptor type 1	0.5491	50
TMDD1	Transmembrane and death domain 1	0.5445	50
KRTAP13-4	Keratin associated protein 13-4	0.5368	50
EBF1	EBF transcription factor 1	0.5359	50
PPDPFL	Pancreatic progenitor cell differentiation and proliferation factor like	0.5310	50
CCN5	Cellular communication network factor 5	0.5295	50
FXYD1	FXYD domain containing ion transport regulator 1	0.5261	2
KLF9	Kruppel like factor 9	0.5159	50
TBX15	T-box transcription factor 15	0.5119	50
C1R	Complement C1r	0.5108	50
PCDHB11	Protocadherin beta 11	0.5101	50
BMERB1	BMERB domain containing 1	0.5098	50
STRIT1	Small transmembrane regulator of ion transport 1	0.5083	50

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	24.5 nTPM
Adipose tissue	26.7 nTPM
Breast	22.3 nTPM

Alveolar cells type 1	38.5 nTPM
Lung	38.5 nTPM

Alveolar cells type 2	25.4 nTPM
Lung	25.4 nTPM

Astrocytes	17.6 nTPM
Brain	17.6 nTPM

B-cells	35.4 nTPM
Lymph node	67.3 nTPM
Adipose tissue	45.6 nTPM
Stomach	38.1 nTPM
PBMC	37.1 nTPM
Liver	34.7 nTPM
Spleen	33.9 nTPM
Bone marrow	32.7 nTPM
Breast	28.1 nTPM
Colon	27.1 nTPM
Kidney	9.5 nTPM

Dendritic cells	42.0 nTPM
Adipose tissue	57.3 nTPM
PBMC	35.8 nTPM
Breast	32.8 nTPM

Endothelial cells	21.7 nTPM
Eye	42.9 nTPM
Heart muscle	39.1 nTPM
Skeletal muscle	27.1 nTPM
Testis	25.8 nTPM
Skin	25.8 nTPM
Breast	24.9 nTPM
Endometrium	21.9 nTPM
Esophagus	20.6 nTPM
Prostate	17.3 nTPM
Liver	15.6 nTPM
Placenta	14.2 nTPM
Ovary	12.9 nTPM
Lung	12.5 nTPM
Pancreas	3.9 nTPM

Fibroblasts	36.7 nTPM
Adipose tissue	109.7 nTPM
Heart muscle	62.3 nTPM
Esophagus	53.6 nTPM
Skeletal muscle	42.2 nTPM
Prostate	28.5 nTPM
Ovary	25.8 nTPM
Breast	22.4 nTPM
Skin	22.3 nTPM
Stomach	19.3 nTPM
Placenta	10.0 nTPM
Lung	7.8 nTPM

Intestinal goblet cells	8.3 nTPM
Small intestine	13.3 nTPM
Rectum	8.1 nTPM
Colon	3.6 nTPM

Macrophages	16.3 nTPM
Spleen	32.1 nTPM
Esophagus	28.3 nTPM
Skeletal muscle	23.9 nTPM
Ovary	23.8 nTPM
Kidney	23.4 nTPM
Adipose tissue	22.6 nTPM
Bone marrow	20.0 nTPM
Breast	19.9 nTPM
Testis	15.7 nTPM
Endometrium	11.3 nTPM
Lung	10.9 nTPM
Prostate	8.1 nTPM
Pancreas	5.1 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	7.8 nTPM
Small intestine	15.0 nTPM
Rectum	8.3 nTPM
Colon	0.0 nTPM

Plasma cells	41.2 nTPM
Esophagus	55.5 nTPM
Adipose tissue	45.2 nTPM
Spleen	40.9 nTPM
Stomach	34.8 nTPM
Bone marrow	29.7 nTPM

Respiratory ciliated cells	29.7 nTPM
Lung	35.0 nTPM
Bronchus	24.4 nTPM

Smooth muscle cells	59.0 nTPM
Adipose tissue	126.3 nTPM
Ovary	103.6 nTPM
Skeletal muscle	88.0 nTPM
Heart muscle	87.7 nTPM
Prostate	64.4 nTPM
Esophagus	58.9 nTPM
Skin	35.6 nTPM
Breast	31.0 nTPM
Endometrium	19.5 nTPM
Bronchus	17.8 nTPM
Pancreas	15.8 nTPM

T-cells	40.9 nTPM
Lymph node	66.6 nTPM
Skeletal muscle	60.2 nTPM
Esophagus	58.9 nTPM
Adipose tissue	57.7 nTPM
PBMC	51.4 nTPM
Liver	50.3 nTPM
Breast	47.7 nTPM
Endometrium	42.7 nTPM
Colon	39.5 nTPM
Spleen	36.8 nTPM
Bone marrow	34.9 nTPM
Kidney	34.2 nTPM
Stomach	32.2 nTPM
Skin	30.4 nTPM
Ovary	24.5 nTPM
Prostate	14.2 nTPM
Lung	13.6 nTPM

Basal keratinocytes	14.9 nTPM
Skin	14.9 nTPM

Basal prostatic cells	16.1 nTPM
Prostate	16.1 nTPM

Basal respiratory cells	4.3 nTPM
Bronchus	4.3 nTPM

Basal squamous epithelial cells	32.5 nTPM
Esophagus	32.5 nTPM

Undifferentiated cells	10.8 nTPM
Small intestine	17.2 nTPM
Rectum	10.1 nTPM
Colon	5.1 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