Single cell type - SLCO4A1 - 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.	SLCO4A1
Gene descriptionⁱ Full gene name according to HGNC.	Solute carrier organic anion transporter family member 4A1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Metabolic proteins 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	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Extravillous trophoblasts - 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 (Extravillous trophoblasts, Adipocytes, Melanocytes)
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	Immune cell enhanced (T-reg)
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 single
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 (PC-3, RPTEC TERT1)
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 many
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, Adipocytes, Melanocytes)

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

SLCO4A1 is part of cluster 38 Extravillous trophoblasts - Unknown function 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
HAPLN3	Hyaluronan and proteoglycan link protein 3	0.7574	38
MACIR	Macrophage immunometabolism regulator	0.7298	38
HLA-G	Major histocompatibility complex, class I, G	0.7207	38
SEPTIN3	Septin 3	0.7194	38
HEY1	Hes related family bHLH transcription factor with YRPW motif 1	0.7163	14
H2BC9	H2B clustered histone 9	0.7159	38
HTRA4	HtrA serine peptidase 4	0.7154	38
TLX3	T cell leukemia homeobox 3	0.7144	38
NLRP9	NLR family pyrin domain containing 9	0.7127	38
LAIR2	Leukocyte associated immunoglobulin like receptor 2	0.7113	38
NOTUM	Notum, palmitoleoyl-protein carboxylesterase	0.7082	38
CCNE1	Cyclin E1	0.7028	38
KISS1R	KISS1 receptor	0.6985	38
FANCE	FA complementation group E	0.6966	38
MTSS2	MTSS I-BAR domain containing 2	0.6940	38

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	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	1.3 nTPM
Lung	1.3 nTPM

Astrocytes	1.3 nTPM
Brain	1.3 nTPM

B-cells	13.1 nTPM
Adipose tissue	49.1 nTPM
Stomach	23.6 nTPM
Colon	20.8 nTPM
Liver	10.8 nTPM
Lymph node	10.3 nTPM
Spleen	8.3 nTPM
Breast	6.6 nTPM
Bone marrow	1.7 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM

Basal keratinocytes	27.3 nTPM
Skin	27.3 nTPM

Dendritic cells	3.7 nTPM
Adipose tissue	8.5 nTPM
Breast	2.5 nTPM
PBMC	0.0 nTPM

Endothelial cells	40.3 nTPM
Skin	104.2 nTPM
Heart muscle	82.4 nTPM
Prostate	78.9 nTPM
Skeletal muscle	76.9 nTPM
Eye	72.8 nTPM
Esophagus	31.1 nTPM
Lung	28.1 nTPM
Liver	24.7 nTPM
Pancreas	19.3 nTPM
Testis	15.7 nTPM
Breast	14.5 nTPM
Endometrium	9.8 nTPM
Placenta	5.1 nTPM
Ovary	0.6 nTPM

Fibroblasts	4.3 nTPM
Stomach	11.9 nTPM
Heart muscle	9.0 nTPM
Prostate	8.4 nTPM
Skin	8.2 nTPM
Lung	4.5 nTPM
Placenta	3.0 nTPM
Skeletal muscle	0.9 nTPM
Esophagus	0.5 nTPM
Breast	0.5 nTPM
Adipose tissue	0.3 nTPM
Ovary	0.1 nTPM

Intestinal goblet cells	8.4 nTPM
Colon	12.1 nTPM
Small intestine	7.8 nTPM
Rectum	5.4 nTPM

Macrophages	11.9 nTPM
Adipose tissue	65.5 nTPM
Esophagus	23.6 nTPM
Testis	23.2 nTPM
Stomach	14.7 nTPM
Skeletal muscle	12.2 nTPM
Pancreas	10.2 nTPM
Prostate	8.1 nTPM
Lung	4.1 nTPM
Endometrium	4.1 nTPM
Breast	3.7 nTPM
Spleen	3.1 nTPM
Kidney	3.0 nTPM
Ovary	1.8 nTPM
Bone marrow	1.2 nTPM
PBMC	0.0 nTPM

Paneth cells	1.9 nTPM
Colon	3.3 nTPM
Rectum	2.5 nTPM
Small intestine	0.0 nTPM

Plasma cells	19.1 nTPM
Adipose tissue	31.0 nTPM
Esophagus	24.6 nTPM
Spleen	14.9 nTPM
Stomach	13.6 nTPM
Bone marrow	11.5 nTPM

Respiratory ciliated cells	1.3 nTPM
Lung	1.5 nTPM
Bronchus	1.1 nTPM

Smooth muscle cells	2.9 nTPM
Heart muscle	13.9 nTPM
Skin	7.7 nTPM
Skeletal muscle	2.5 nTPM
Bronchus	2.0 nTPM
Endometrium	1.6 nTPM
Esophagus	1.5 nTPM
Prostate	0.9 nTPM
Pancreas	0.6 nTPM
Breast	0.5 nTPM
Ovary	0.2 nTPM
Adipose tissue	0.0 nTPM

T-cells	5.6 nTPM
Esophagus	19.7 nTPM
Skin	11.6 nTPM
Adipose tissue	10.5 nTPM
Prostate	9.5 nTPM
Stomach	8.6 nTPM
Colon	8.5 nTPM
Breast	7.1 nTPM
Endometrium	6.6 nTPM
Skeletal muscle	3.0 nTPM
Lymph node	3.0 nTPM
Liver	1.9 nTPM
Lung	1.5 nTPM
Spleen	1.5 nTPM
Kidney	0.7 nTPM
Bone marrow	0.5 nTPM
PBMC	0.3 nTPM
Ovary	0.0 nTPM

Collecting duct cells	25.8 nTPM
Kidney	25.8 nTPM

Cone photoreceptor cells	31.3 nTPM
Eye	31.3 nTPM

Cytotrophoblasts	2.1 nTPM
Placenta	2.1 nTPM

Endometrial stromal cells	3.6 nTPM
Endometrium	3.6 nTPM

Undifferentiated cells	7.5 nTPM
Small intestine	10.4 nTPM
Colon	7.8 nTPM
Rectum	4.4 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