Single cell type - TSFM - 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.	TSFM
Gene descriptionⁱ Full gene name according to HGNC.	Ts translation elongation factor, mitochondrial
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	8

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 - Basic cellular processes (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 (Proximal tubular 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	Cell line enriched (RH-30)
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 (Proximal tubular 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

TSFM is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 1
586 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
METTL1	Methyltransferase like 1	0.5930	67
ACOT13	Acyl-CoA thioesterase 13	0.5914	29
PCCB	Propionyl-CoA carboxylase subunit beta	0.5753	29
CYP27B1	Cytochrome P450 family 27 subfamily B member 1	0.5729	67
PES1	Pescadillo ribosomal biogenesis factor 1	0.5545	39
MRPL40	Mitochondrial ribosomal protein L40	0.5480	39
MRPL2	Mitochondrial ribosomal protein L2	0.5438	10
GATD3B	Glutamine amidotransferase like class 1 domain containing 3B	0.5422	67
POLDIP2	DNA polymerase delta interacting protein 2	0.5385	39
MALSU1	Mitochondrial assembly of ribosomal large subunit 1	0.5261	10
ZSCAN2	Zinc finger and SCAN domain containing 2	0.5229	67
EEF1E1	Eukaryotic translation elongation factor 1 epsilon 1	0.5185	34
EEF1AKMT4	EEF1A lysine methyltransferase 4	0.5170	7
GCAT	Glycine C-acetyltransferase	0.5137	67
COQ6	Coenzyme Q6, monooxygenase	0.5126	29

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	16.5 nTPM
Breast	23.4 nTPM
Adipose tissue	9.7 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	10.8 nTPM
Lung	10.8 nTPM

Astrocytes	6.2 nTPM
Brain	6.2 nTPM

B-cells	18.5 nTPM
Liver	38.5 nTPM
PBMC	22.8 nTPM
Colon	19.2 nTPM
Spleen	19.0 nTPM
Breast	18.7 nTPM
Bone marrow	18.0 nTPM
Lymph node	15.4 nTPM
Stomach	14.5 nTPM
Kidney	14.3 nTPM
Adipose tissue	4.5 nTPM

Dendritic cells	23.5 nTPM
PBMC	31.8 nTPM
Adipose tissue	20.2 nTPM
Breast	18.6 nTPM

Endothelial cells	18.7 nTPM
Pancreas	50.2 nTPM
Placenta	31.8 nTPM
Ovary	27.7 nTPM
Testis	24.9 nTPM
Endometrium	18.3 nTPM
Skin	17.5 nTPM
Breast	15.5 nTPM
Esophagus	14.5 nTPM
Prostate	14.1 nTPM
Skeletal muscle	14.1 nTPM
Lung	9.3 nTPM
Liver	9.2 nTPM
Eye	8.1 nTPM
Heart muscle	7.2 nTPM

Fibroblasts	18.8 nTPM
Ovary	39.1 nTPM
Placenta	27.6 nTPM
Lung	22.4 nTPM
Prostate	17.9 nTPM
Skeletal muscle	17.3 nTPM
Breast	16.7 nTPM
Skin	15.5 nTPM
Adipose tissue	15.1 nTPM
Esophagus	13.3 nTPM
Heart muscle	11.6 nTPM
Stomach	10.4 nTPM

Intestinal goblet cells	20.9 nTPM
Colon	25.7 nTPM
Small intestine	19.2 nTPM
Rectum	17.7 nTPM

Macrophages	18.1 nTPM
Pancreas	81.7 nTPM
Kidney	35.6 nTPM
Testis	26.1 nTPM
Ovary	19.5 nTPM
Lung	16.7 nTPM
Esophagus	15.8 nTPM
Breast	14.5 nTPM
Bone marrow	12.5 nTPM
Endometrium	10.9 nTPM
Spleen	10.4 nTPM
Stomach	8.8 nTPM
Skeletal muscle	8.2 nTPM
Adipose tissue	6.2 nTPM
Prostate	4.6 nTPM
PBMC	0.0 nTPM

Paneth cells	15.7 nTPM
Rectum	21.8 nTPM
Small intestine	18.8 nTPM
Colon	6.5 nTPM

Plasma cells	17.5 nTPM
Spleen	27.0 nTPM
Bone marrow	24.7 nTPM
Stomach	18.9 nTPM
Esophagus	12.3 nTPM
Adipose tissue	4.5 nTPM

Respiratory ciliated cells	26.0 nTPM
Bronchus	30.1 nTPM
Lung	21.9 nTPM

Smooth muscle cells	31.6 nTPM
Bronchus	118.7 nTPM
Pancreas	57.0 nTPM
Ovary	34.9 nTPM
Esophagus	21.7 nTPM
Breast	20.6 nTPM
Skin	19.9 nTPM
Heart muscle	18.9 nTPM
Endometrium	16.2 nTPM
Skeletal muscle	15.7 nTPM
Prostate	13.1 nTPM
Adipose tissue	11.0 nTPM

T-cells	18.6 nTPM
Kidney	29.4 nTPM
Colon	28.5 nTPM
Esophagus	26.2 nTPM
PBMC	24.1 nTPM
Liver	23.2 nTPM
Ovary	20.1 nTPM
Stomach	18.5 nTPM
Bone marrow	17.9 nTPM
Lymph node	17.1 nTPM
Skin	16.6 nTPM
Breast	16.1 nTPM
Adipose tissue	15.9 nTPM
Spleen	15.5 nTPM
Endometrium	13.9 nTPM
Skeletal muscle	12.4 nTPM
Lung	10.6 nTPM
Prostate	9.5 nTPM

Basal keratinocytes	25.9 nTPM
Skin	25.9 nTPM

Basal respiratory cells	57.4 nTPM
Bronchus	57.4 nTPM

Cholangiocytes	27.1 nTPM
Liver	27.1 nTPM

Collecting duct cells	46.0 nTPM
Kidney	46.0 nTPM

Undifferentiated cells	35.3 nTPM
Colon	37.4 nTPM
Small intestine	37.4 nTPM
Rectum	31.0 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