Single cell type - PSD4 - 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.	PSD4
Gene descriptionⁱ Full gene name according to HGNC.	Pleckstrin and Sec7 domain containing 4
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.	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	NK-cells & T-cells - Immune response (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 (Hepatocytes, Proximal enterocytes)
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	Cell line enhanced (Daudi, NB-4)
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 (Hepatocytes, Proximal enterocytes)

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

PSD4 is part of cluster 63 NK-cells & T-cells - Immune response with confidenceⁱ 1
362 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
PATL2	PAT1 homolog 2	0.7114	63
SASH3	SAM and SH3 domain containing 3	0.6856	63
RINL	Ras and Rab interactor like	0.6592	63
TBC1D10C	TBC1 domain family member 10C	0.6551	63
FCRL3	Fc receptor like 3	0.6531	57
SUN2	Sad1 and UNC84 domain containing 2	0.6410	63
NCR3	Natural cytotoxicity triggering receptor 3	0.6363	63
IL16	Interleukin 16	0.6316	63
APOBEC3D	Apolipoprotein B mRNA editing enzyme catalytic subunit 3D	0.6270	63
SLAMF6	SLAM family member 6	0.6243	63
DENND1C	DENN domain containing 1C	0.6115	63
CARD11	Caspase recruitment domain family member 11	0.6045	57
DENND2D	DENN domain containing 2D	0.6008	63
TMIGD2	Transmembrane and immunoglobulin domain containing 2	0.6007	63
NLRC3	NLR family CARD domain containing 3	0.6005	63

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	0.9 nTPM
Breast	1.2 nTPM
Adipose tissue	0.7 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	12.0 nTPM
Lung	12.0 nTPM

Astrocytes	7.5 nTPM
Brain	7.5 nTPM

B-cells	28.6 nTPM
Lymph node	43.6 nTPM
PBMC	40.0 nTPM
Bone marrow	37.6 nTPM
Stomach	33.6 nTPM
Spleen	30.1 nTPM
Liver	25.9 nTPM
Colon	25.5 nTPM
Kidney	19.0 nTPM
Breast	17.3 nTPM
Adipose tissue	13.5 nTPM

Dendritic cells	41.6 nTPM
PBMC	59.8 nTPM
Breast	37.1 nTPM
Adipose tissue	27.9 nTPM

Endothelial cells	2.1 nTPM
Lung	6.2 nTPM
Pancreas	3.9 nTPM
Eye	3.3 nTPM
Skin	2.5 nTPM
Breast	2.5 nTPM
Skeletal muscle	2.2 nTPM
Prostate	2.0 nTPM
Heart muscle	1.8 nTPM
Liver	1.8 nTPM
Endometrium	1.3 nTPM
Testis	1.1 nTPM
Placenta	0.6 nTPM
Esophagus	0.6 nTPM
Ovary	0.3 nTPM

Fibroblasts	3.0 nTPM
Lung	16.8 nTPM
Stomach	3.0 nTPM
Placenta	2.6 nTPM
Prostate	2.4 nTPM
Skin	2.2 nTPM
Breast	1.9 nTPM
Heart muscle	1.5 nTPM
Ovary	1.1 nTPM
Skeletal muscle	1.0 nTPM
Adipose tissue	0.3 nTPM
Esophagus	0.3 nTPM

Intestinal goblet cells	10.7 nTPM
Rectum	12.3 nTPM
Small intestine	12.0 nTPM
Colon	7.8 nTPM

Macrophages	14.3 nTPM
Spleen	20.7 nTPM
Kidney	19.6 nTPM
Stomach	17.6 nTPM
Endometrium	17.5 nTPM
Esophagus	15.8 nTPM
Skeletal muscle	15.5 nTPM
Lung	14.1 nTPM
PBMC	13.6 nTPM
Breast	13.3 nTPM
Pancreas	12.8 nTPM
Prostate	12.6 nTPM
Adipose tissue	12.4 nTPM
Testis	11.1 nTPM
Ovary	9.9 nTPM
Bone marrow	8.7 nTPM

Paneth cells	17.8 nTPM
Colon	23.1 nTPM
Rectum	15.3 nTPM
Small intestine	15.0 nTPM

Plasma cells	18.3 nTPM
Adipose tissue	29.1 nTPM
Stomach	20.1 nTPM
Esophagus	18.4 nTPM
Bone marrow	13.2 nTPM
Spleen	10.7 nTPM

Respiratory ciliated cells	4.6 nTPM
Bronchus	4.9 nTPM
Lung	4.4 nTPM

Smooth muscle cells	1.7 nTPM
Skin	3.1 nTPM
Esophagus	3.1 nTPM
Heart muscle	2.5 nTPM
Breast	2.4 nTPM
Pancreas	1.8 nTPM
Skeletal muscle	1.7 nTPM
Endometrium	1.5 nTPM
Bronchus	1.0 nTPM
Prostate	0.9 nTPM
Ovary	0.7 nTPM
Adipose tissue	0.6 nTPM

T-cells	28.2 nTPM
Stomach	55.9 nTPM
Liver	47.2 nTPM
Bone marrow	44.7 nTPM
Endometrium	37.8 nTPM
Spleen	36.6 nTPM
PBMC	33.7 nTPM
Lymph node	32.1 nTPM
Colon	29.0 nTPM
Breast	28.9 nTPM
Skeletal muscle	27.1 nTPM
Ovary	24.5 nTPM
Kidney	21.2 nTPM
Skin	19.8 nTPM
Lung	19.7 nTPM
Adipose tissue	14.7 nTPM
Esophagus	6.6 nTPM
Prostate	0.0 nTPM

Basal keratinocytes	12.7 nTPM
Skin	12.7 nTPM

Basal prostatic cells	10.4 nTPM
Prostate	10.4 nTPM

Basal respiratory cells	7.6 nTPM
Bronchus	7.6 nTPM

Basal squamous epithelial cells	13.1 nTPM
Esophagus	13.1 nTPM

Undifferentiated cells	18.6 nTPM
Small intestine	19.2 nTPM
Colon	19.0 nTPM
Rectum	17.5 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