Single cell type - SPEN - 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.	SPEN
Gene descriptionⁱ Full gene name according to HGNC.	Spen family transcriptional repressor
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes 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.	4

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	Endometrium - Transcription (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

SPEN is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
ZNF592	Zinc finger protein 592	0.7253	44
NUP153	Nucleoporin 153	0.7141	44
KMT2C	Lysine methyltransferase 2C	0.7108	44
PHACTR4	Phosphatase and actin regulator 4	0.7094	44
ZBTB11	Zinc finger and BTB domain containing 11	0.7087	44
USP9X	Ubiquitin specific peptidase 9 X-linked	0.6565	44
AVPR1B	Arginine vasopressin receptor 1B	0.6496	44
MMP26	Matrix metallopeptidase 26	0.6429	44
AL353572.3	Novel protein	0.6320	44
RC3H1	Ring finger and CCCH-type domains 1	0.6277	44
SNIP1	Smad nuclear interacting protein 1	0.6195	44
OR51L1	Olfactory receptor family 51 subfamily L member 1	0.6143	44
ALPG	Alkaline phosphatase, germ cell	0.6114	44
OR5AU1	Olfactory receptor family 5 subfamily AU member 1	0.6113	44
RCOR1	REST corepressor 1	0.6093	44

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	55.7 nTPM
Adipose tissue	58.8 nTPM
Breast	52.7 nTPM

Alveolar cells type 1	80.1 nTPM
Lung	80.1 nTPM

Alveolar cells type 2	85.3 nTPM
Lung	85.3 nTPM

Astrocytes	68.9 nTPM
Brain	68.9 nTPM

B-cells	69.4 nTPM
Lymph node	112.2 nTPM
Adipose tissue	96.2 nTPM
Stomach	91.7 nTPM
Bone marrow	82.5 nTPM
Spleen	80.9 nTPM
PBMC	65.7 nTPM
Breast	53.6 nTPM
Colon	46.4 nTPM
Kidney	38.1 nTPM
Liver	26.6 nTPM

Dendritic cells	52.8 nTPM
Adipose tissue	74.9 nTPM
Breast	59.4 nTPM
PBMC	23.9 nTPM

Endothelial cells	51.6 nTPM
Endometrium	102.8 nTPM
Heart muscle	81.1 nTPM
Skin	75.1 nTPM
Eye	74.4 nTPM
Prostate	68.4 nTPM
Skeletal muscle	65.4 nTPM
Esophagus	54.8 nTPM
Ovary	46.3 nTPM
Lung	43.7 nTPM
Breast	41.5 nTPM
Liver	31.2 nTPM
Testis	27.5 nTPM
Placenta	10.2 nTPM
Pancreas	0.0 nTPM

Fibroblasts	45.9 nTPM
Heart muscle	106.7 nTPM
Skin	78.2 nTPM
Lung	54.7 nTPM
Prostate	50.7 nTPM
Skeletal muscle	46.1 nTPM
Adipose tissue	36.5 nTPM
Ovary	33.2 nTPM
Stomach	31.2 nTPM
Esophagus	30.1 nTPM
Breast	26.9 nTPM
Placenta	10.7 nTPM

Intestinal goblet cells	27.4 nTPM
Colon	31.5 nTPM
Small intestine	28.4 nTPM
Rectum	22.3 nTPM

Macrophages	53.2 nTPM
Esophagus	83.4 nTPM
Skeletal muscle	81.7 nTPM
Adipose tissue	81.7 nTPM
Bone marrow	81.2 nTPM
Lung	75.4 nTPM
Endometrium	74.8 nTPM
Ovary	61.9 nTPM
Breast	58.8 nTPM
Spleen	56.0 nTPM
Stomach	55.7 nTPM
Testis	28.4 nTPM
Prostate	26.3 nTPM
Kidney	22.7 nTPM
Pancreas	10.2 nTPM
PBMC	0.0 nTPM

Paneth cells	34.6 nTPM
Colon	59.3 nTPM
Rectum	25.6 nTPM
Small intestine	18.8 nTPM

Plasma cells	74.5 nTPM
Adipose tissue	129.0 nTPM
Esophagus	67.8 nTPM
Spleen	60.8 nTPM
Bone marrow	57.7 nTPM
Stomach	57.4 nTPM

Respiratory ciliated cells	29.4 nTPM
Lung	42.3 nTPM
Bronchus	16.4 nTPM

Smooth muscle cells	56.6 nTPM
Endometrium	104.7 nTPM
Heart muscle	84.6 nTPM
Adipose tissue	68.2 nTPM
Esophagus	66.7 nTPM
Skeletal muscle	66.6 nTPM
Skin	61.0 nTPM
Breast	51.9 nTPM
Prostate	51.0 nTPM
Ovary	37.2 nTPM
Bronchus	15.9 nTPM
Pancreas	14.8 nTPM

T-cells	52.3 nTPM
Endometrium	89.0 nTPM
Skeletal muscle	86.4 nTPM
Lymph node	68.5 nTPM
Adipose tissue	65.9 nTPM
Breast	64.1 nTPM
Ovary	60.1 nTPM
Skin	58.5 nTPM
Colon	58.0 nTPM
Lung	54.6 nTPM
Spleen	52.2 nTPM
Stomach	47.5 nTPM
Bone marrow	46.8 nTPM
Esophagus	45.9 nTPM
PBMC	40.3 nTPM
Liver	25.6 nTPM
Kidney	15.8 nTPM
Prostate	9.5 nTPM

Basal keratinocytes	104.6 nTPM
Skin	104.6 nTPM

Basal prostatic cells	44.9 nTPM
Prostate	44.9 nTPM

Basal respiratory cells	18.3 nTPM
Bronchus	18.3 nTPM

Basal squamous epithelial cells	90.5 nTPM
Esophagus	90.5 nTPM

Undifferentiated cells	32.8 nTPM
Colon	55.0 nTPM
Rectum	22.4 nTPM
Small intestine	20.8 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