Single cell type - TM6SF1 - 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.	TM6SF1
Gene descriptionⁱ Full gene name according to HGNC.	Transmembrane 6 superfamily member 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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.	5

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 - Unknown function (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 (Hofbauer cells, Microglial cells, Langerhans cells, Macrophages, granulocytes, Kupffer cells, Adipocytes)
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	Group enriched (eosinophil, neutrophil, basophil)
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	Cell line enhanced (HEL, HHSteC, HUVEC TERT2, JURKAT, TIME, U-698)
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: Cell type enhanced (Hofbauer cells, Microglial cells, Langerhans cells, Macrophages, granulocytes, Kupffer cells, Adipocytes)

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

TM6SF1 is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 1
482 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
LTC4S	Leukotriene C4 synthase	0.6490	10
NCF4	Neutrophil cytosolic factor 4	0.6167	57
TRPM2	Transient receptor potential cation channel subfamily M member 2	0.5875	21
F13A1	Coagulation factor XIII A chain	0.5805	4
RAB39A	RAB39A, member RAS oncogene family	0.5747	8
KCNK13	Potassium two pore domain channel subfamily K member 13	0.5740	10
FES	FES proto-oncogene, tyrosine kinase	0.5642	10
MEF2A	Myocyte enhancer factor 2A	0.5544	10
GPR34	G protein-coupled receptor 34	0.5401	4
FGF20	Fibroblast growth factor 20	0.5383	41
MYO5A	Myosin VA	0.5360	42
PICALM	Phosphatidylinositol binding clathrin assembly protein	0.5339	10
SRGAP2	SLIT-ROBO Rho GTPase activating protein 2	0.5339	41
BMP2K	BMP2 inducible kinase	0.5238	4
STAB1	Stabilin 1	0.5237	4

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

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	6.0 nTPM
Lung	6.0 nTPM

Astrocytes	2.9 nTPM
Brain	2.9 nTPM

B-cells	0.9 nTPM
Colon	3.2 nTPM
Lymph node	1.6 nTPM
PBMC	1.4 nTPM
Spleen	1.0 nTPM
Stomach	0.9 nTPM
Liver	0.4 nTPM
Kidney	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Breast	0.0 nTPM

Basal keratinocytes	2.4 nTPM
Skin	2.4 nTPM

Dendritic cells	7.5 nTPM
Breast	13.1 nTPM
Adipose tissue	9.3 nTPM
PBMC	0.0 nTPM

Endothelial cells	16.7 nTPM
Testis	66.3 nTPM
Esophagus	26.4 nTPM
Skeletal muscle	25.3 nTPM
Liver	17.4 nTPM
Eye	15.4 nTPM
Skin	14.1 nTPM
Breast	14.0 nTPM
Pancreas	11.6 nTPM
Placenta	11.3 nTPM
Lung	9.3 nTPM
Prostate	8.2 nTPM
Heart muscle	5.0 nTPM
Ovary	4.8 nTPM
Endometrium	4.5 nTPM

Fibroblasts	1.5 nTPM
Stomach	7.4 nTPM
Lung	4.5 nTPM
Skin	1.3 nTPM
Breast	1.2 nTPM
Placenta	0.7 nTPM
Heart muscle	0.5 nTPM
Skeletal muscle	0.5 nTPM
Prostate	0.2 nTPM
Ovary	0.2 nTPM
Adipose tissue	0.2 nTPM
Esophagus	0.2 nTPM

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

Macrophages	45.9 nTPM
Testis	91.8 nTPM
Breast	83.5 nTPM
PBMC	81.8 nTPM
Esophagus	70.8 nTPM
Adipose tissue	59.8 nTPM
Prostate	49.2 nTPM
Pancreas	46.0 nTPM
Lung	40.8 nTPM
Ovary	37.2 nTPM
Skeletal muscle	25.2 nTPM
Spleen	24.9 nTPM
Stomach	23.5 nTPM
Kidney	20.4 nTPM
Bone marrow	18.8 nTPM
Endometrium	15.3 nTPM

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

Plasma cells	0.7 nTPM
Adipose tissue	3.3 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	1.4 nTPM
Lung	1.5 nTPM
Bronchus	1.3 nTPM

Smooth muscle cells	0.6 nTPM
Breast	1.6 nTPM
Pancreas	1.5 nTPM
Skin	1.1 nTPM
Skeletal muscle	0.9 nTPM
Heart muscle	0.4 nTPM
Prostate	0.4 nTPM
Endometrium	0.4 nTPM
Adipose tissue	0.4 nTPM
Bronchus	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	4.2 nTPM
Prostate	14.2 nTPM
Ovary	13.4 nTPM
Lung	10.6 nTPM
Esophagus	6.6 nTPM
Liver	4.2 nTPM
Bone marrow	4.1 nTPM
Colon	2.9 nTPM
Spleen	2.6 nTPM
PBMC	2.5 nTPM
Endometrium	2.1 nTPM
Kidney	2.0 nTPM
Breast	1.9 nTPM
Stomach	1.6 nTPM
Skeletal muscle	1.5 nTPM
Adipose tissue	0.7 nTPM
Skin	0.5 nTPM
Lymph node	0.4 nTPM

Cytotrophoblasts	0.3 nTPM
Placenta	0.3 nTPM

Excitatory neurons	18.7 nTPM
Brain	18.7 nTPM

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