Single cell type - PDCD6IP - 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.	PDCD6IP
Gene descriptionⁱ Full gene name according to HGNC.	Programmed cell death 6 interacting protein
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.	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	Intestinal epithelial cells - 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 (Distal 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 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 (Distal 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

PDCD6IP is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
MUC12	Mucin 12, cell surface associated	0.7900	53
GPA33	Glycoprotein A33	0.7851	53
MS4A12	Membrane spanning 4-domains A12	0.7849	53
SLC26A3	Solute carrier family 26 member 3	0.7845	53
CEACAM7	CEA cell adhesion molecule 7	0.7800	53
GCNT3	Glucosaminyl (N-acetyl) transferase 3, mucin type	0.7663	53
CASP7	Caspase 7	0.7586	53
CD177	CD177 molecule	0.7566	53
TMEM54	Transmembrane protein 54	0.7564	53
HRCT1	Histidine rich carboxyl terminus 1	0.7477	53
AQP8	Aquaporin 8	0.7464	53
CEACAM5	CEA cell adhesion molecule 5	0.7378	53
HHLA2	HERV-H LTR-associating 2	0.7368	53
SCNN1B	Sodium channel epithelial 1 subunit beta	0.7337	53
ETHE1	ETHE1 persulfide dioxygenase	0.7296	53

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	78.5 nTPM
Adipose tissue	97.4 nTPM
Breast	59.6 nTPM

Alveolar cells type 1	86.6 nTPM
Lung	86.6 nTPM

Alveolar cells type 2	84.8 nTPM
Lung	84.8 nTPM

Astrocytes	85.8 nTPM
Brain	85.8 nTPM

B-cells	76.1 nTPM
Stomach	122.1 nTPM
Adipose tissue	108.2 nTPM
Bone marrow	100.6 nTPM
Spleen	92.7 nTPM
Lymph node	90.5 nTPM
PBMC	71.3 nTPM
Breast	50.9 nTPM
Colon	49.5 nTPM
Kidney	42.9 nTPM
Liver	31.8 nTPM

Dendritic cells	58.5 nTPM
Adipose tissue	73.2 nTPM
PBMC	59.8 nTPM
Breast	42.7 nTPM

Endothelial cells	68.8 nTPM
Lung	137.3 nTPM
Heart muscle	81.4 nTPM
Skeletal muscle	80.3 nTPM
Testis	78.5 nTPM
Ovary	77.9 nTPM
Endometrium	71.4 nTPM
Esophagus	66.0 nTPM
Placenta	64.2 nTPM
Prostate	60.8 nTPM
Skin	54.2 nTPM
Breast	52.9 nTPM
Pancreas	50.2 nTPM
Eye	46.1 nTPM
Liver	42.2 nTPM

Fibroblasts	54.3 nTPM
Adipose tissue	79.6 nTPM
Lung	69.2 nTPM
Skeletal muscle	60.7 nTPM
Stomach	57.9 nTPM
Breast	55.8 nTPM
Heart muscle	49.8 nTPM
Esophagus	48.5 nTPM
Skin	47.9 nTPM
Prostate	45.4 nTPM
Placenta	42.6 nTPM
Ovary	40.1 nTPM

Intestinal goblet cells	97.1 nTPM
Rectum	102.3 nTPM
Colon	100.1 nTPM
Small intestine	88.9 nTPM

Macrophages	85.0 nTPM
Lung	137.6 nTPM
Stomach	120.1 nTPM
Spleen	119.2 nTPM
Adipose tissue	110.1 nTPM
Ovary	93.6 nTPM
Bone marrow	92.4 nTPM
Pancreas	91.9 nTPM
Testis	87.2 nTPM
Skeletal muscle	86.9 nTPM
Endometrium	72.1 nTPM
Kidney	68.8 nTPM
Esophagus	67.7 nTPM
Prostate	58.5 nTPM
Breast	55.8 nTPM
PBMC	13.6 nTPM

Paneth cells	127.1 nTPM
Colon	217.4 nTPM
Rectum	100.2 nTPM
Small intestine	63.8 nTPM

Plasma cells	46.9 nTPM
Adipose tissue	71.6 nTPM
Stomach	61.6 nTPM
Spleen	40.6 nTPM
Bone marrow	36.2 nTPM
Esophagus	24.6 nTPM

Respiratory ciliated cells	130.9 nTPM
Bronchus	139.4 nTPM
Lung	122.4 nTPM

Smooth muscle cells	50.4 nTPM
Pancreas	68.2 nTPM
Bronchus	65.1 nTPM
Ovary	60.1 nTPM
Adipose tissue	56.8 nTPM
Endometrium	51.9 nTPM
Esophagus	48.0 nTPM
Prostate	43.5 nTPM
Heart muscle	42.6 nTPM
Breast	41.8 nTPM
Skeletal muscle	39.9 nTPM
Skin	37.1 nTPM

T-cells	55.2 nTPM
Stomach	80.8 nTPM
Adipose tissue	80.2 nTPM
Lung	77.5 nTPM
Spleen	72.9 nTPM
Lymph node	71.4 nTPM
Bone marrow	68.0 nTPM
Endometrium	58.1 nTPM
Skeletal muscle	53.7 nTPM
Colon	52.7 nTPM
Breast	49.3 nTPM
PBMC	48.4 nTPM
Liver	44.9 nTPM
Prostate	42.6 nTPM
Kidney	41.1 nTPM
Skin	38.2 nTPM
Esophagus	32.8 nTPM
Ovary	26.7 nTPM

Basal keratinocytes	41.7 nTPM
Skin	41.7 nTPM

Basal prostatic cells	62.6 nTPM
Prostate	62.6 nTPM

Basal respiratory cells	62.7 nTPM
Bronchus	62.7 nTPM

Cholangiocytes	62.9 nTPM
Liver	62.9 nTPM

Undifferentiated cells	86.7 nTPM
Colon	112.7 nTPM
Rectum	84.8 nTPM
Small intestine	62.7 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