Single cell type - PCF11 - 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.	PCF11
Gene descriptionⁱ Full gene name according to HGNC.	PCF11 cleavage and polyadenylation factor subunit
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.	5

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	Non-specific - Mitochondria (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 (Skeletal myocytes)
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	Cell line enhanced (U-698)
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 (Skeletal myocytes)

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

PCF11 is part of cluster 7 Non-specific - Mitochondria with confidenceⁱ 1
481 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
ING1	Inhibitor of growth family member 1	0.6585	7
INTS6	Integrator complex subunit 6	0.6571	7
SIRT1	Sirtuin 1	0.6457	7
ERO1B	Endoplasmic reticulum oxidoreductase 1 beta	0.6280	7
CYB5D1	Cytochrome b5 domain containing 1	0.6167	7
NUFIP2	Nuclear FMR1 interacting protein 2	0.6066	7
FOSB	FosB proto-oncogene, AP-1 transcription factor subunit	0.6019	7
ARIH1	Ariadne RBR E3 ubiquitin protein ligase 1	0.5910	7
TOPORS	TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase	0.5683	29
PPP1R10	Protein phosphatase 1 regulatory subunit 10	0.5637	7
CALCR	Calcitonin receptor	0.5600	50
POLG2	DNA polymerase gamma 2, accessory subunit	0.5520	7
HEXIM1	HEXIM P-TEFb complex subunit 1	0.5491	7
MIDN	Midnolin	0.5373	7
PRX	Periaxin	0.5352	14

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	96.4 nTPM
Adipose tissue	108.5 nTPM
Breast	84.3 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	63.5 nTPM
Lung	63.5 nTPM

Astrocytes	58.1 nTPM
Brain	58.1 nTPM

B-cells	90.6 nTPM
Lymph node	168.5 nTPM
Breast	132.4 nTPM
Adipose tissue	119.8 nTPM
PBMC	104.2 nTPM
Spleen	83.0 nTPM
Kidney	71.4 nTPM
Bone marrow	67.0 nTPM
Stomach	64.1 nTPM
Colon	47.9 nTPM
Liver	47.6 nTPM

Basal squamous epithelial cells	101.9 nTPM
Esophagus	101.9 nTPM

Dendritic cells	90.1 nTPM
Breast	103.6 nTPM
Adipose tissue	95.0 nTPM
PBMC	71.8 nTPM

Endothelial cells	66.8 nTPM
Skeletal muscle	129.6 nTPM
Prostate	118.1 nTPM
Eye	93.1 nTPM
Breast	84.3 nTPM
Endometrium	69.8 nTPM
Heart muscle	68.7 nTPM
Esophagus	59.9 nTPM
Liver	59.6 nTPM
Lung	59.3 nTPM
Testis	58.1 nTPM
Skin	51.3 nTPM
Ovary	42.8 nTPM
Placenta	36.4 nTPM
Pancreas	3.9 nTPM

Fibroblasts	58.8 nTPM
Prostate	109.8 nTPM
Heart muscle	81.4 nTPM
Skeletal muscle	75.5 nTPM
Adipose tissue	66.1 nTPM
Breast	63.6 nTPM
Esophagus	62.9 nTPM
Stomach	50.5 nTPM
Skin	48.7 nTPM
Ovary	31.9 nTPM
Lung	30.1 nTPM
Placenta	26.6 nTPM

Intestinal goblet cells	51.0 nTPM
Small intestine	53.8 nTPM
Colon	53.6 nTPM
Rectum	45.5 nTPM

Macrophages	87.4 nTPM
Adipose tissue	154.7 nTPM
Breast	139.9 nTPM
Skeletal muscle	139.8 nTPM
Spleen	134.8 nTPM
Testis	94.7 nTPM
Endometrium	94.3 nTPM
Esophagus	91.2 nTPM
Prostate	88.3 nTPM
Stomach	85.0 nTPM
Kidney	56.7 nTPM
Lung	54.5 nTPM
Bone marrow	53.7 nTPM
Ovary	49.2 nTPM
PBMC	40.9 nTPM
Pancreas	33.2 nTPM

Paneth cells	46.2 nTPM
Rectum	60.8 nTPM
Small intestine	45.0 nTPM
Colon	32.9 nTPM

Plasma cells	69.0 nTPM
Adipose tissue	94.8 nTPM
Esophagus	80.1 nTPM
Bone marrow	62.6 nTPM
Spleen	54.7 nTPM
Stomach	52.7 nTPM

Respiratory ciliated cells	29.0 nTPM
Bronchus	30.3 nTPM
Lung	27.7 nTPM

Smooth muscle cells	66.8 nTPM
Skeletal muscle	127.1 nTPM
Prostate	98.4 nTPM
Adipose tissue	84.0 nTPM
Endometrium	74.3 nTPM
Breast	74.3 nTPM
Heart muscle	72.4 nTPM
Skin	61.4 nTPM
Esophagus	58.9 nTPM
Ovary	38.9 nTPM
Bronchus	29.1 nTPM
Pancreas	15.7 nTPM

Cholangiocytes	35.8 nTPM
Liver	35.8 nTPM

Collecting duct cells	46.0 nTPM
Kidney	46.0 nTPM

Cone photoreceptor cells	33.3 nTPM
Eye	33.3 nTPM

Cytotrophoblasts	30.2 nTPM
Placenta	30.2 nTPM

T-cells	81.7 nTPM
Breast	145.6 nTPM
Lymph node	137.3 nTPM
Skeletal muscle	135.3 nTPM
Endometrium	116.5 nTPM
Prostate	99.4 nTPM
Adipose tissue	92.8 nTPM
Liver	81.7 nTPM
PBMC	79.9 nTPM
Kidney	75.3 nTPM
Esophagus	72.0 nTPM
Lung	71.4 nTPM
Spleen	71.1 nTPM
Bone marrow	47.3 nTPM
Skin	43.7 nTPM
Stomach	43.7 nTPM
Colon	40.4 nTPM
Ovary	35.6 nTPM

Undifferentiated cells	50.3 nTPM
Small intestine	54.6 nTPM
Colon	50.5 nTPM
Rectum	45.8 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