Single cell type - PDCD7 - 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.	PDCD7
Gene descriptionⁱ Full gene name according to HGNC.	Programmed cell death 7
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.	2

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	Photoreceptor cells - Phototransduction (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 (Cone photoreceptor cells, Rod photoreceptor cells, Bipolar cells, Spermatocytes)
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: Cell type enhanced (Cone photoreceptor cells, Rod photoreceptor cells, Bipolar cells, Spermatocytes)

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

PDCD7 is part of cluster 9 Photoreceptor cells - Phototransduction with confidenceⁱ 0.91
227 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
TRIM44	Tripartite motif containing 44	0.6509	9
GNB3	G protein subunit beta 3	0.6072	9
RD3	Retinal degeneration 3, GUCY2D regulator	0.6042	9
CACNA1F	Calcium voltage-gated channel subunit alpha1 F	0.6012	9
NTNG2	Netrin G2	0.5622	9
PLCD4	Phospholipase C delta 4	0.5553	9
CCDC177	Coiled-coil domain containing 177	0.5527	56
SLC12A5	Solute carrier family 12 member 5	0.5514	9
OTX2	Orthodenticle homeobox 2	0.5503	9
ZNF517	Zinc finger protein 517	0.5471	22
ISL2	ISL LIM homeobox 2	0.5420	9
RGS11	Regulator of G protein signaling 11	0.5318	9
BBS4	Bardet-Biedl syndrome 4	0.5315	9
RIC3	RIC3 acetylcholine receptor chaperone	0.5313	52
CIART	Circadian associated repressor of transcription	0.5290	9

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	33.6 nTPM
Breast	36.9 nTPM
Adipose tissue	30.4 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	14.3 nTPM
Lung	14.3 nTPM

Astrocytes	10.1 nTPM
Brain	10.1 nTPM

B-cells	46.3 nTPM
Adipose tissue	68.2 nTPM
Stomach	59.0 nTPM
Breast	57.5 nTPM
Lymph node	45.4 nTPM
Bone marrow	44.2 nTPM
Spleen	43.3 nTPM
PBMC	40.0 nTPM
Colon	36.7 nTPM
Liver	35.5 nTPM
Kidney	33.4 nTPM

Dendritic cells	55.8 nTPM
Adipose tissue	77.9 nTPM
Breast	61.6 nTPM
PBMC	27.9 nTPM

Endothelial cells	36.5 nTPM
Prostate	58.2 nTPM
Liver	52.2 nTPM
Eye	48.6 nTPM
Esophagus	46.8 nTPM
Testis	46.2 nTPM
Endometrium	44.3 nTPM
Breast	40.9 nTPM
Ovary	37.2 nTPM
Skeletal muscle	36.8 nTPM
Skin	31.8 nTPM
Heart muscle	24.9 nTPM
Placenta	24.5 nTPM
Pancreas	11.6 nTPM
Lung	6.2 nTPM

Fibroblasts	38.4 nTPM
Prostate	65.8 nTPM
Ovary	58.9 nTPM
Adipose tissue	48.4 nTPM
Esophagus	48.3 nTPM
Breast	43.0 nTPM
Skeletal muscle	37.2 nTPM
Skin	32.6 nTPM
Placenta	31.6 nTPM
Stomach	28.2 nTPM
Lung	17.9 nTPM
Heart muscle	10.7 nTPM

Intestinal goblet cells	26.9 nTPM
Colon	41.4 nTPM
Rectum	20.4 nTPM
Small intestine	18.9 nTPM

Macrophages	24.7 nTPM
Breast	42.9 nTPM
Ovary	40.6 nTPM
Kidney	34.0 nTPM
Testis	33.7 nTPM
Bone marrow	32.4 nTPM
Adipose tissue	32.2 nTPM
Endometrium	28.0 nTPM
Skeletal muscle	27.7 nTPM
Prostate	22.9 nTPM
Spleen	22.8 nTPM
Esophagus	20.4 nTPM
Pancreas	15.3 nTPM
Stomach	8.8 nTPM
Lung	8.7 nTPM
PBMC	0.0 nTPM

Paneth cells	11.6 nTPM
Rectum	17.0 nTPM
Small intestine	11.3 nTPM
Colon	6.5 nTPM

Plasma cells	37.9 nTPM
Adipose tissue	50.3 nTPM
Esophagus	49.4 nTPM
Spleen	35.2 nTPM
Stomach	28.3 nTPM
Bone marrow	26.4 nTPM

Respiratory ciliated cells	8.5 nTPM
Lung	10.2 nTPM
Bronchus	6.8 nTPM

Smooth muscle cells	38.8 nTPM
Ovary	75.9 nTPM
Prostate	61.8 nTPM
Endometrium	49.4 nTPM
Esophagus	46.5 nTPM
Adipose tissue	45.0 nTPM
Skeletal muscle	39.2 nTPM
Breast	36.7 nTPM
Pancreas	28.4 nTPM
Skin	26.2 nTPM
Heart muscle	13.1 nTPM
Bronchus	4.7 nTPM

T-cells	49.5 nTPM
Adipose tissue	74.5 nTPM
Breast	70.2 nTPM
Kidney	67.1 nTPM
Ovary	66.8 nTPM
Skeletal muscle	64.0 nTPM
Prostate	61.6 nTPM
PBMC	56.8 nTPM
Liver	52.1 nTPM
Endometrium	50.7 nTPM
Colon	47.5 nTPM
Lymph node	44.4 nTPM
Stomach	41.9 nTPM
Spleen	40.4 nTPM
Bone marrow	38.0 nTPM
Skin	29.9 nTPM
Esophagus	26.2 nTPM
Lung	9.1 nTPM

Basal prostatic cells	67.8 nTPM
Prostate	67.8 nTPM

Basal respiratory cells	6.0 nTPM
Bronchus	6.0 nTPM

Basal squamous epithelial cells	89.4 nTPM
Esophagus	89.4 nTPM

Cholangiocytes	21.5 nTPM
Liver	21.5 nTPM

Undifferentiated cells	26.1 nTPM
Small intestine	29.6 nTPM
Colon	26.8 nTPM
Rectum	21.8 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