Single cell type - EDEM3 - 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.	EDEM3
Gene descriptionⁱ Full gene name according to HGNC.	ER degradation enhancing alpha-mannosidase like protein 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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	Mucus-secreting cells - Mucin production (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 many
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

EDEM3 is part of cluster 27 Mucus-secreting cells - Mucin production with confidenceⁱ 1
121 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
GFPT1	Glutamine--fructose-6-phosphate transaminase 1	0.5921	27
ZG16	Zymogen granule protein 16	0.5638	27
FFAR4	Free fatty acid receptor 4	0.5637	27
FCGBP	Fc fragment of IgG binding protein	0.5607	27
BEST2	Bestrophin 2	0.5587	27
ITLN1	Intelectin 1	0.5580	27
ATOH1	Atonal bHLH transcription factor 1	0.5509	27
REP15	RAB15 effector protein	0.5500	27
LRRC31	Leucine rich repeat containing 31	0.5490	27
B3GNT6	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6	0.5474	27
TFF3	Trefoil factor 3	0.5437	27
TPSG1	Tryptase gamma 1	0.5407	27
BCAS1	Brain enriched myelin associated protein 1	0.5401	27
ANO7	Anoctamin 7	0.5306	27
TBX10	T-box transcription factor 10	0.5226	27

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	35.1 nTPM
Adipose tissue	46.2 nTPM
Breast	24.0 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	19.3 nTPM
Lung	19.3 nTPM

Astrocytes	41.4 nTPM
Brain	41.4 nTPM

B-cells	19.9 nTPM
Spleen	35.0 nTPM
Bone marrow	30.2 nTPM
Breast	29.4 nTPM
Lymph node	26.3 nTPM
Liver	18.9 nTPM
Stomach	18.2 nTPM
Adipose tissue	15.0 nTPM
PBMC	11.5 nTPM
Colon	9.6 nTPM
Kidney	4.8 nTPM

Dendritic cells	13.2 nTPM
Breast	16.0 nTPM
Adipose tissue	15.5 nTPM
PBMC	8.0 nTPM

Endothelial cells	25.9 nTPM
Prostate	48.4 nTPM
Heart muscle	48.3 nTPM
Skin	32.7 nTPM
Eye	30.7 nTPM
Endometrium	29.6 nTPM
Skeletal muscle	27.3 nTPM
Esophagus	24.1 nTPM
Ovary	23.0 nTPM
Breast	22.2 nTPM
Liver	22.0 nTPM
Lung	21.8 nTPM
Testis	15.4 nTPM
Placenta	13.7 nTPM
Pancreas	3.9 nTPM

Fibroblasts	28.0 nTPM
Stomach	40.1 nTPM
Skeletal muscle	32.4 nTPM
Adipose tissue	31.2 nTPM
Esophagus	29.8 nTPM
Prostate	29.6 nTPM
Lung	26.8 nTPM
Ovary	26.5 nTPM
Skin	26.3 nTPM
Heart muscle	22.8 nTPM
Placenta	21.5 nTPM
Breast	21.5 nTPM

Intestinal goblet cells	76.5 nTPM
Rectum	98.1 nTPM
Colon	88.6 nTPM
Small intestine	42.8 nTPM

Macrophages	33.0 nTPM
Stomach	64.5 nTPM
Spleen	58.1 nTPM
Esophagus	45.6 nTPM
Skeletal muscle	45.1 nTPM
Bone marrow	43.7 nTPM
Adipose tissue	41.1 nTPM
Testis	38.3 nTPM
Ovary	36.6 nTPM
Lung	27.3 nTPM
Endometrium	21.2 nTPM
Kidney	21.1 nTPM
Pancreas	20.4 nTPM
Breast	17.0 nTPM
Prostate	15.0 nTPM
PBMC	0.0 nTPM

Paneth cells	28.1 nTPM
Rectum	42.1 nTPM
Small intestine	22.5 nTPM
Colon	19.7 nTPM

Plasma cells	73.6 nTPM
Stomach	119.6 nTPM
Esophagus	104.7 nTPM
Bone marrow	56.0 nTPM
Spleen	53.0 nTPM
Adipose tissue	34.9 nTPM

Respiratory ciliated cells	28.1 nTPM
Bronchus	31.5 nTPM
Lung	24.8 nTPM

Smooth muscle cells	18.7 nTPM
Esophagus	24.8 nTPM
Endometrium	22.9 nTPM
Adipose tissue	22.4 nTPM
Skeletal muscle	20.9 nTPM
Prostate	20.0 nTPM
Bronchus	19.8 nTPM
Heart muscle	19.1 nTPM
Pancreas	16.0 nTPM
Breast	13.5 nTPM
Skin	13.3 nTPM
Ovary	13.1 nTPM

T-cells	24.9 nTPM
Esophagus	65.5 nTPM
Bone marrow	36.4 nTPM
Lymph node	35.4 nTPM
Stomach	33.0 nTPM
Spleen	32.6 nTPM
Adipose tissue	26.8 nTPM
Skin	24.4 nTPM
Colon	23.7 nTPM
Skeletal muscle	22.9 nTPM
PBMC	19.9 nTPM
Lung	19.7 nTPM
Breast	19.7 nTPM
Endometrium	18.0 nTPM
Ovary	15.6 nTPM
Prostate	14.2 nTPM
Liver	10.7 nTPM
Kidney	4.7 nTPM

Basal keratinocytes	16.7 nTPM
Skin	16.7 nTPM

Basal prostatic cells	8.4 nTPM
Prostate	8.4 nTPM

Basal respiratory cells	9.8 nTPM
Bronchus	9.8 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Undifferentiated cells	32.4 nTPM
Rectum	40.7 nTPM
Colon	34.1 nTPM
Small intestine	22.5 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