Single cell type - EML3 - 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.	EML3
Gene descriptionⁱ Full gene name according to HGNC.	EMAP like 3
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.	10

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	Squamous epithelial cells - 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	Cell type enhanced (Squamous epithelial 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	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: Cell type enhanced (Squamous epithelial 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

EML3 is part of cluster 61 Squamous epithelial cells - Keratinization with confidenceⁱ 1
176 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
SPINK7	Serine peptidase inhibitor Kazal type 7	0.7142	61
CRNN	Cornulin	0.7125	61
LTB4R2	Leukotriene B4 receptor 2	0.7123	59
KRT6C	Keratin 6C	0.7011	61
KRT4	Keratin 4	0.6989	61
MRPS24	Mitochondrial ribosomal protein S24	0.6978	59
MC5R	Melanocortin 5 receptor	0.6975	61
SPRR3	Small proline rich protein 3	0.6970	61
PGLYRP3	Peptidoglycan recognition protein 3	0.6964	61
NME2	NME/NM23 nucleoside diphosphate kinase 2	0.6915	61
PDF	Peptide deformylase, mitochondrial	0.6889	59
GBP6	Guanylate binding protein family member 6	0.6865	61
RHCG	Rh family C glycoprotein	0.6810	61
KRT13	Keratin 13	0.6796	61
CALML3	Calmodulin like 3	0.6727	61

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	29.8 nTPM
Adipose tissue	32.2 nTPM
Breast	27.4 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	14.5 nTPM
Lung	14.5 nTPM

Astrocytes	15.3 nTPM
Brain	15.3 nTPM

B-cells	18.5 nTPM
Stomach	31.8 nTPM
Lymph node	29.2 nTPM
Bone marrow	22.9 nTPM
Spleen	22.5 nTPM
Liver	19.9 nTPM
Colon	14.4 nTPM
Kidney	14.3 nTPM
Adipose tissue	12.0 nTPM
PBMC	9.9 nTPM
Breast	8.1 nTPM

Dendritic cells	14.0 nTPM
Breast	21.8 nTPM
Adipose tissue	16.1 nTPM
PBMC	4.0 nTPM

Endothelial cells	27.0 nTPM
Testis	46.8 nTPM
Esophagus	46.5 nTPM
Ovary	35.2 nTPM
Liver	33.0 nTPM
Breast	27.8 nTPM
Pancreas	27.0 nTPM
Placenta	26.7 nTPM
Heart muscle	26.3 nTPM
Skeletal muscle	25.5 nTPM
Endometrium	21.3 nTPM
Prostate	18.4 nTPM
Eye	17.0 nTPM
Skin	14.3 nTPM
Lung	12.5 nTPM

Fibroblasts	12.8 nTPM
Heart muscle	19.8 nTPM
Esophagus	16.8 nTPM
Stomach	14.9 nTPM
Breast	14.1 nTPM
Skin	12.8 nTPM
Placenta	11.8 nTPM
Prostate	11.8 nTPM
Lung	11.1 nTPM
Skeletal muscle	10.1 nTPM
Ovary	9.2 nTPM
Adipose tissue	8.2 nTPM

Intestinal goblet cells	11.0 nTPM
Rectum	14.6 nTPM
Small intestine	10.5 nTPM
Colon	7.8 nTPM

Macrophages	16.7 nTPM
Stomach	38.1 nTPM
Spleen	37.4 nTPM
Bone marrow	23.7 nTPM
Skeletal muscle	19.7 nTPM
Lung	16.8 nTPM
Adipose tissue	16.1 nTPM
Breast	15.4 nTPM
Kidney	15.2 nTPM
Testis	14.0 nTPM
Pancreas	12.8 nTPM
Esophagus	12.6 nTPM
Endometrium	12.3 nTPM
Ovary	11.2 nTPM
Prostate	5.7 nTPM
PBMC	0.0 nTPM

Paneth cells	11.5 nTPM
Rectum	17.2 nTPM
Colon	9.9 nTPM
Small intestine	7.5 nTPM

Plasma cells	15.9 nTPM
Esophagus	18.4 nTPM
Adipose tissue	17.4 nTPM
Bone marrow	16.5 nTPM
Spleen	14.4 nTPM
Stomach	13.0 nTPM

Respiratory ciliated cells	7.6 nTPM
Bronchus	10.8 nTPM
Lung	4.4 nTPM

Smooth muscle cells	12.8 nTPM
Esophagus	17.0 nTPM
Adipose tissue	15.8 nTPM
Skeletal muscle	15.4 nTPM
Heart muscle	14.7 nTPM
Breast	14.6 nTPM
Ovary	13.8 nTPM
Pancreas	13.1 nTPM
Skin	11.9 nTPM
Prostate	10.6 nTPM
Endometrium	7.7 nTPM
Bronchus	6.6 nTPM

T-cells	23.5 nTPM
Stomach	43.4 nTPM
Esophagus	39.3 nTPM
Bone marrow	34.1 nTPM
Lymph node	34.0 nTPM
Spleen	31.6 nTPM
Liver	28.3 nTPM
Breast	22.9 nTPM
Kidney	21.2 nTPM
Skin	20.7 nTPM
Skeletal muscle	19.6 nTPM
Prostate	19.0 nTPM
Colon	16.1 nTPM
PBMC	15.3 nTPM
Adipose tissue	14.6 nTPM
Endometrium	13.9 nTPM
Ovary	13.4 nTPM
Lung	12.2 nTPM

Basal prostatic cells	12.1 nTPM
Prostate	12.1 nTPM

Cholangiocytes	15.7 nTPM
Liver	15.7 nTPM

Cone photoreceptor cells	8.4 nTPM
Eye	8.4 nTPM

Distal tubular cells	5.9 nTPM
Kidney	5.9 nTPM

Undifferentiated cells	10.3 nTPM
Rectum	13.3 nTPM
Colon	9.4 nTPM
Small intestine	8.2 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