Single cell type - SELENOF - 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.	SELENOF
Gene descriptionⁱ Full gene name according to HGNC.	Selenoprotein F
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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.	6

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 - Mitochondria (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 (Extravillous trophoblasts, Syncytiotrophoblasts, Cytotrophoblasts, Hofbauer cells, Ductal 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 (Extravillous trophoblasts, Syncytiotrophoblasts, Cytotrophoblasts, Hofbauer cells, Ductal 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

SELENOF is part of cluster 7 Non-specific - Mitochondria with confidenceⁱ 1
481 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
MCRIP1	MAPK regulated corepressor interacting protein 1	0.8158	7
ELOC	Elongin C	0.8156	7
SELENOT	Selenoprotein T	0.7978	7
BUD23	BUD23 rRNA methyltransferase and ribosome maturation factor	0.7951	7
RTF2	Replication termination factor 2	0.7693	7
INTS11	Integrator complex subunit 11	0.7664	7
HIKESHI	Heat shock protein nuclear import factor hikeshi	0.7519	7
UTP11	UTP11 small subunit processome component	0.7501	7
UFD1	Ubiquitin recognition factor in ER associated degradation 1	0.7446	7
STMP1	Short transmembrane mitochondrial protein 1	0.7363	7
SELENOH	Selenoprotein H	0.7341	7
ELOB	Elongin B	0.7292	7
NBDY	Negative regulator of P-body association	0.7282	7
INTS13	Integrator complex subunit 13	0.7188	7
DMAC2	Distal membrane arm assembly complex 2	0.7176	7

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	131.6 nTPM
Breast	140.6 nTPM
Adipose tissue	122.6 nTPM

Alveolar cells type 1	118.6 nTPM
Lung	118.6 nTPM

Alveolar cells type 2	155.2 nTPM
Lung	155.2 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	52.4 nTPM
Kidney	238.1 nTPM
Breast	149.7 nTPM
Adipose tissue	136.3 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	89.3 nTPM
Breast	161.4 nTPM
Adipose tissue	106.5 nTPM
PBMC	0.0 nTPM

Endothelial cells	73.2 nTPM
Pancreas	262.5 nTPM
Placenta	208.6 nTPM
Lung	180.9 nTPM
Breast	152.8 nTPM
Ovary	113.0 nTPM
Endometrium	107.2 nTPM
Eye	0.0 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Prostate	0.0 nTPM
Testis	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM

Fibroblasts	85.2 nTPM
Placenta	302.3 nTPM
Breast	207.3 nTPM
Adipose tissue	182.7 nTPM
Lung	145.2 nTPM
Ovary	99.9 nTPM
Heart muscle	0.0 nTPM
Prostate	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM

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

Macrophages	78.1 nTPM
Pancreas	280.8 nTPM
Lung	192.5 nTPM
Kidney	192.0 nTPM
Adipose tissue	144.4 nTPM
Ovary	126.5 nTPM
Breast	123.6 nTPM
Endometrium	111.1 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

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

Plasma cells	19.1 nTPM
Adipose tissue	95.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	70.0 nTPM
Lung	139.9 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	61.5 nTPM
Pancreas	271.6 nTPM
Breast	112.2 nTPM
Ovary	107.0 nTPM
Adipose tissue	105.7 nTPM
Endometrium	79.8 nTPM
Heart muscle	0.0 nTPM
Prostate	0.0 nTPM
Skin	0.0 nTPM
Bronchus	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	53.9 nTPM
Kidney	232.1 nTPM
Lung	174.7 nTPM
Ovary	151.2 nTPM
Breast	148.1 nTPM
Adipose tissue	117.1 nTPM
Endometrium	92.3 nTPM
Colon	0.0 nTPM
Liver	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Collecting duct cells	108.5 nTPM
Kidney	108.5 nTPM

Cytotrophoblasts	248.6 nTPM
Placenta	248.6 nTPM

Endometrial stromal cells	119.1 nTPM
Endometrium	119.1 nTPM

Exocrine glandular cells	193.5 nTPM
Pancreas	193.5 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