Single cell type - NCL - 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.	NCL
Gene descriptionⁱ Full gene name according to HGNC.	Nucleolin
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.	11

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 - 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	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

NCL is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 0.98
482 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
HNRNPAB	Heterogeneous nuclear ribonucleoprotein A/B	0.7120	10
MAK16	MAK16 homolog	0.6975	10
NOP56	NOP56 ribonucleoprotein	0.6745	10
SET	SET nuclear proto-oncogene	0.6305	39
NOP14	NOP14 nucleolar protein	0.6267	10
NOLC1	Nucleolar and coiled-body phosphoprotein 1	0.6218	39
NOP58	NOP58 ribonucleoprotein	0.6190	10
SYNCRIP	Synaptotagmin binding cytoplasmic RNA interacting protein	0.6182	10
RBM25	RNA binding motif protein 25	0.6104	52
NIFK	Nucleolar protein interacting with the FHA domain of MKI67	0.6042	39
SRRM1	Serine and arginine repetitive matrix 1	0.6005	52
POLE3	DNA polymerase epsilon 3, accessory subunit	0.5996	39
SMNDC1	Survival motor neuron domain containing 1	0.5958	10
PRPF40A	Pre-mRNA processing factor 40 homolog A	0.5899	10
CCDC137	Coiled-coil domain containing 137	0.5832	39

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	286.2 nTPM
Adipose tissue	288.3 nTPM
Breast	284.2 nTPM

Alveolar cells type 1	291.7 nTPM
Lung	291.7 nTPM

Alveolar cells type 2	411.7 nTPM
Lung	411.7 nTPM

Astrocytes	8.1 nTPM
Brain	8.1 nTPM

B-cells	468.9 nTPM
Adipose tissue	857.7 nTPM
Lymph node	614.9 nTPM
Stomach	564.9 nTPM
Spleen	521.5 nTPM
Breast	436.0 nTPM
Liver	432.7 nTPM
Bone marrow	365.4 nTPM
Colon	346.6 nTPM
PBMC	296.9 nTPM
Kidney	252.3 nTPM

Basal squamous epithelial cells	644.9 nTPM
Esophagus	644.9 nTPM

Dendritic cells	596.2 nTPM
Adipose tissue	1023.9 nTPM
Breast	537.6 nTPM
PBMC	227.1 nTPM

Endothelial cells	291.1 nTPM
Prostate	544.3 nTPM
Lung	452.2 nTPM
Endometrium	413.0 nTPM
Esophagus	365.0 nTPM
Breast	288.8 nTPM
Pancreas	274.1 nTPM
Skin	246.6 nTPM
Placenta	246.1 nTPM
Ovary	240.9 nTPM
Skeletal muscle	238.4 nTPM
Heart muscle	211.2 nTPM
Eye	202.3 nTPM
Testis	178.1 nTPM
Liver	174.3 nTPM

Enteroendocrine cells	200.0 nTPM
Colon	266.5 nTPM
Rectum	133.5 nTPM

Erythroid cells	419.2 nTPM
Bone marrow	656.5 nTPM
Liver	181.9 nTPM

Fibroblasts	370.9 nTPM
Lung	927.1 nTPM
Prostate	484.4 nTPM
Ovary	384.0 nTPM
Stomach	335.6 nTPM
Heart muscle	325.2 nTPM
Placenta	299.9 nTPM
Adipose tissue	298.0 nTPM
Esophagus	295.5 nTPM
Breast	272.1 nTPM
Skeletal muscle	235.8 nTPM
Skin	222.5 nTPM

Intestinal goblet cells	319.6 nTPM
Colon	594.7 nTPM
Rectum	183.5 nTPM
Small intestine	180.7 nTPM

Macrophages	281.8 nTPM
Adipose tissue	545.2 nTPM
Endometrium	536.1 nTPM
Lung	467.6 nTPM
Breast	417.6 nTPM
Esophagus	384.0 nTPM
Kidney	254.8 nTPM
Skeletal muscle	245.7 nTPM
Spleen	214.7 nTPM
Bone marrow	206.1 nTPM
Stomach	199.3 nTPM
Pancreas	191.4 nTPM
Testis	182.9 nTPM
Prostate	176.6 nTPM
Ovary	164.2 nTPM
PBMC	40.9 nTPM

Paneth cells	153.9 nTPM
Rectum	194.9 nTPM
Colon	158.1 nTPM
Small intestine	108.8 nTPM

Plasma cells	543.5 nTPM
Bone marrow	662.5 nTPM
Spleen	600.5 nTPM
Adipose tissue	506.3 nTPM
Stomach	492.2 nTPM
Esophagus	455.8 nTPM

Cholangiocytes	147.3 nTPM
Liver	147.3 nTPM

Collecting duct cells	195.0 nTPM
Kidney	195.0 nTPM

Cone photoreceptor cells	47.9 nTPM
Eye	47.9 nTPM

Cytotrophoblasts	386.9 nTPM
Placenta	386.9 nTPM

Respiratory ciliated cells	250.3 nTPM
Lung	419.8 nTPM
Bronchus	80.8 nTPM

Smooth muscle cells	442.0 nTPM
Bronchus	1011.2 nTPM
Endometrium	489.7 nTPM
Prostate	481.7 nTPM
Ovary	434.7 nTPM
Esophagus	395.4 nTPM
Skeletal muscle	378.9 nTPM
Heart muscle	368.8 nTPM
Adipose tissue	360.7 nTPM
Breast	333.3 nTPM
Pancreas	326.9 nTPM
Skin	281.1 nTPM

T-cells	454.0 nTPM
Adipose tissue	969.1 nTPM
Endometrium	705.9 nTPM
Lymph node	559.5 nTPM
Breast	537.4 nTPM
Lung	533.0 nTPM
Skeletal muscle	528.1 nTPM
Stomach	518.8 nTPM
Prostate	449.7 nTPM
Colon	412.9 nTPM
Spleen	410.8 nTPM
Esophagus	406.1 nTPM
PBMC	335.0 nTPM
Bone marrow	334.6 nTPM
Ovary	318.1 nTPM
Kidney	271.0 nTPM
Skin	250.0 nTPM
Liver	178.1 nTPM

Undifferentiated cells	380.6 nTPM
Colon	626.7 nTPM
Small intestine	283.0 nTPM
Rectum	232.2 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