Single cell type - JAML - 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.	JAML
Gene descriptionⁱ Full gene name according to HGNC.	Junction adhesion molecule like
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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Monocytes & Neutrophils - Innate immune response (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	Group enriched (monocytes, Macrophages, dendritic cells, Kupffer cells, T-cells)
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	Immune cell enhanced (eosinophil)
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 enriched (HMC-1)
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 some
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: Group enriched (monocytes, Macrophages, dendritic cells, Kupffer cells, T-cells)

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

JAML is part of cluster 19 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 1
175 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
MNDA	Myeloid cell nuclear differentiation antigen	0.8299	19
CCR2	C-C motif chemokine receptor 2	0.8083	19
NLRP12	NLR family pyrin domain containing 12	0.7543	19
CD300LB	CD300 molecule like family member b	0.7520	19
SIRPB1	Signal regulatory protein beta 1	0.7407	19
CLEC4A	C-type lectin domain family 4 member A	0.7365	19
CLEC4D	C-type lectin domain family 4 member D	0.7324	19
LILRA2	Leukocyte immunoglobulin like receptor A2	0.7285	19
PRAM1	PML-RARA regulated adaptor molecule 1	0.7261	19
FCN1	Ficolin 1	0.7261	19
TLR8	Toll like receptor 8	0.7089	19
IL17RA	Interleukin 17 receptor A	0.7082	19
CTSS	Cathepsin S	0.7067	19
SAMHD1	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1	0.7019	19
PADI4	Peptidyl arginine deiminase 4	0.6998	19

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	1.2 nTPM
Breast	2.1 nTPM
Adipose tissue	0.2 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	34.2 nTPM
Lung	34.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	6.9 nTPM
Kidney	23.8 nTPM
PBMC	22.8 nTPM
Liver	7.6 nTPM
Breast	6.6 nTPM
Lymph node	3.2 nTPM
Adipose tissue	2.5 nTPM
Spleen	1.4 nTPM
Stomach	0.9 nTPM
Colon	0.0 nTPM
Bone marrow	0.0 nTPM

Dendritic cells	136.9 nTPM
PBMC	398.5 nTPM
Adipose tissue	7.3 nTPM
Breast	5.1 nTPM

Endothelial cells	1.3 nTPM
Eye	6.5 nTPM
Liver	4.6 nTPM
Lung	3.1 nTPM
Breast	1.3 nTPM
Placenta	1.1 nTPM
Esophagus	1.0 nTPM
Skeletal muscle	0.6 nTPM
Testis	0.3 nTPM
Endometrium	0.2 nTPM
Ovary	0.1 nTPM
Heart muscle	0.0 nTPM
Prostate	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM

Fibroblasts	1.8 nTPM
Lung	13.4 nTPM
Placenta	1.5 nTPM
Stomach	1.5 nTPM
Breast	1.1 nTPM
Prostate	0.7 nTPM
Esophagus	0.6 nTPM
Skeletal muscle	0.5 nTPM
Adipose tissue	0.1 nTPM
Heart muscle	0.0 nTPM
Skin	0.0 nTPM
Ovary	0.0 nTPM

Intestinal goblet cells	0.2 nTPM
Rectum	0.5 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Macrophages	166.6 nTPM
Lung	331.1 nTPM
Kidney	303.3 nTPM
Adipose tissue	206.6 nTPM
Endometrium	206.0 nTPM
Testis	205.7 nTPM
Prostate	196.0 nTPM
Skeletal muscle	189.6 nTPM
Stomach	149.5 nTPM
Spleen	136.9 nTPM
Bone marrow	116.2 nTPM
Pancreas	114.9 nTPM
Ovary	97.7 nTPM
Breast	95.9 nTPM
Esophagus	81.8 nTPM
PBMC	68.2 nTPM

Paneth cells	0.1 nTPM
Rectum	0.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	6.3 nTPM
Adipose tissue	25.2 nTPM
Bone marrow	3.3 nTPM
Stomach	2.5 nTPM
Spleen	0.3 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	2.2 nTPM
Lung	4.4 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	0.5 nTPM
Breast	2.9 nTPM
Esophagus	1.5 nTPM
Endometrium	0.6 nTPM
Skeletal muscle	0.3 nTPM
Ovary	0.2 nTPM
Heart muscle	0.0 nTPM
Prostate	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Bronchus	0.0 nTPM
Adipose tissue	0.0 nTPM

T-cells	56.0 nTPM
Lung	176.1 nTPM
Liver	94.9 nTPM
Stomach	87.4 nTPM
PBMC	82.5 nTPM
Breast	81.3 nTPM
Prostate	71.1 nTPM
Ovary	69.0 nTPM
Adipose tissue	53.2 nTPM
Kidney	48.6 nTPM
Lymph node	37.8 nTPM
Bone marrow	37.1 nTPM
Esophagus	32.8 nTPM
Endometrium	29.3 nTPM
Spleen	27.1 nTPM
Skeletal muscle	23.6 nTPM
Colon	0.0 nTPM
Skin	0.0 nTPM

Cholangiocytes	2.8 nTPM
Liver	2.8 nTPM

Undifferentiated cells	0.1 nTPM
Rectum	0.2 nTPM
Small intestine	0.1 nTPM
Colon	0.0 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