Single cell type - TCOF1 - 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.	TCOF1
Gene descriptionⁱ Full gene name according to HGNC.	Treacle ribosome biogenesis factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes 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.	14

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	Macrophages - 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	Low cell type specificity
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: Low cell type specificity

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

TCOF1 is part of cluster 41 Macrophages - Immune response with confidenceⁱ 1
307 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
TRABD	TraB domain containing	0.5579	39
HLA-DMA	Major histocompatibility complex, class II, DM alpha	0.5545	41
RNASE6	Ribonuclease A family member k6	0.5258	41
CCDC88B	Coiled-coil domain containing 88B	0.5248	63
HLA-DPA1	Major histocompatibility complex, class II, DP alpha 1	0.5189	41
HLA-DRB1	Major histocompatibility complex, class II, DR beta 1	0.5159	41
CIITA	Class II major histocompatibility complex transactivator	0.5097	41
HLA-DOA	Major histocompatibility complex, class II, DO alpha	0.5073	41
IFNA14	Interferon alpha 14	0.5011	41
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1	0.5009	41
HLA-DQA1	Major histocompatibility complex, class II, DQ alpha 1	0.4955	41
COQ7	Coenzyme Q7, hydroxylase	0.4942	45
SRSF3	Serine and arginine rich splicing factor 3	0.4918	7
HLA-DPB1	Major histocompatibility complex, class II, DP beta 1	0.4900	41
TOR3A	Torsin family 3 member A	0.4900	55

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	18.5 nTPM
Breast	19.6 nTPM
Adipose tissue	17.4 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	22.4 nTPM
Lung	22.4 nTPM

Astrocytes	7.8 nTPM
Brain	7.8 nTPM

B-cells	41.7 nTPM
PBMC	81.4 nTPM
Breast	64.1 nTPM
Adipose tissue	50.1 nTPM
Liver	47.8 nTPM
Colon	39.9 nTPM
Kidney	28.5 nTPM
Spleen	28.0 nTPM
Stomach	26.3 nTPM
Lymph node	25.8 nTPM
Bone marrow	25.3 nTPM

Dendritic cells	29.7 nTPM
PBMC	35.8 nTPM
Breast	28.8 nTPM
Adipose tissue	24.4 nTPM

Endothelial cells	24.4 nTPM
Eye	67.2 nTPM
Skeletal muscle	52.1 nTPM
Skin	26.7 nTPM
Prostate	22.4 nTPM
Testis	22.0 nTPM
Ovary	21.6 nTPM
Breast	21.4 nTPM
Endometrium	21.2 nTPM
Lung	18.7 nTPM
Placenta	18.2 nTPM
Heart muscle	16.2 nTPM
Pancreas	15.5 nTPM
Esophagus	9.8 nTPM
Liver	9.2 nTPM

Fibroblasts	20.1 nTPM
Lung	45.8 nTPM
Ovary	30.8 nTPM
Placenta	22.6 nTPM
Heart muscle	20.6 nTPM
Prostate	20.1 nTPM
Skin	18.2 nTPM
Skeletal muscle	15.7 nTPM
Adipose tissue	12.1 nTPM
Stomach	11.9 nTPM
Breast	11.7 nTPM
Esophagus	11.5 nTPM

Intestinal goblet cells	18.8 nTPM
Colon	23.5 nTPM
Small intestine	19.0 nTPM
Rectum	14.0 nTPM

Macrophages	40.0 nTPM
Breast	133.0 nTPM
Endometrium	110.7 nTPM
Skeletal muscle	73.5 nTPM
Adipose tissue	48.1 nTPM
Testis	47.0 nTPM
Kidney	46.2 nTPM
Ovary	29.6 nTPM
Lung	27.7 nTPM
Bone marrow	17.5 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM
Prostate	12.6 nTPM
Spleen	11.4 nTPM
Esophagus	11.0 nTPM
Stomach	5.9 nTPM

Paneth cells	8.4 nTPM
Rectum	11.6 nTPM
Colon	9.9 nTPM
Small intestine	3.7 nTPM

Plasma cells	26.1 nTPM
Spleen	33.6 nTPM
Adipose tissue	31.0 nTPM
Bone marrow	29.7 nTPM
Esophagus	18.4 nTPM
Stomach	17.8 nTPM

Respiratory ciliated cells	10.1 nTPM
Lung	10.2 nTPM
Bronchus	9.9 nTPM

Smooth muscle cells	17.7 nTPM
Pancreas	27.2 nTPM
Heart muscle	24.7 nTPM
Ovary	21.3 nTPM
Skin	20.6 nTPM
Endometrium	20.6 nTPM
Prostate	17.8 nTPM
Skeletal muscle	16.9 nTPM
Esophagus	15.5 nTPM
Breast	13.3 nTPM
Adipose tissue	11.4 nTPM
Bronchus	5.7 nTPM

T-cells	26.3 nTPM
Lung	47.1 nTPM
Skeletal muscle	43.0 nTPM
PBMC	33.4 nTPM
Liver	32.8 nTPM
Endometrium	31.9 nTPM
Breast	29.7 nTPM
Kidney	28.7 nTPM
Bone marrow	27.2 nTPM
Spleen	25.8 nTPM
Adipose tissue	25.5 nTPM
Lymph node	25.0 nTPM
Stomach	23.7 nTPM
Colon	22.8 nTPM
Ovary	20.1 nTPM
Skin	18.8 nTPM
Esophagus	6.6 nTPM
Prostate	4.7 nTPM

Basal prostatic cells	21.1 nTPM
Prostate	21.1 nTPM

Basal respiratory cells	14.5 nTPM
Bronchus	14.5 nTPM

Basal squamous epithelial cells	15.9 nTPM
Esophagus	15.9 nTPM

Cytotrophoblasts	21.7 nTPM
Placenta	21.7 nTPM

Undifferentiated cells	32.0 nTPM
Colon	50.9 nTPM
Small intestine	23.3 nTPM
Rectum	22.0 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