Single cell type - NEDD8 - 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.	NEDD8
Gene descriptionⁱ Full gene name according to HGNC.	NEDD8 ubiquitin like modifier
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-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.	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	Pancreatic endocrine cells - Mixed 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

NEDD8 is part of cluster 16 Pancreatic endocrine cells - Mixed function with confidenceⁱ 1
171 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
SUMO1	Small ubiquitin like modifier 1	0.6507	10
NOP10	NOP10 ribonucleoprotein	0.6483	10
S100A11	S100 calcium binding protein A11	0.6324	16
RBX1	Ring-box 1	0.6024	6
SERPINB7	Serpin family B member 7	0.5905	16
SPRR1B	Small proline rich protein 1B	0.5900	16
SSBP1	Single stranded DNA binding protein 1	0.5827	26
CLIC1	Chloride intracellular channel 1	0.5807	16
MYL12B	Myosin light chain 12B	0.5776	16
FAM25C	Family with sequence similarity 25 member C	0.5730	16
MRPS21	Mitochondrial ribosomal protein S21	0.5723	39
VPS29	VPS29 retromer complex component	0.5697	10
PGK1	Phosphoglycerate kinase 1	0.5682	26
TBCA	Tubulin folding cofactor A	0.5645	2
DEFB4A	Defensin beta 4A	0.5594	16

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	276.4 nTPM
Breast	337.5 nTPM
Adipose tissue	215.3 nTPM

Alveolar cells type 1	144.2 nTPM
Lung	144.2 nTPM

Alveolar cells type 2	156.8 nTPM
Lung	156.8 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	182.1 nTPM
Liver	323.6 nTPM
Kidney	295.2 nTPM
PBMC	232.7 nTPM
Colon	217.3 nTPM
Spleen	146.0 nTPM
Bone marrow	133.2 nTPM
Breast	125.8 nTPM
Adipose tissue	118.9 nTPM
Lymph node	114.4 nTPM
Stomach	113.5 nTPM

Basal squamous epithelial cells	166.8 nTPM
Esophagus	166.8 nTPM

Dendritic cells	237.0 nTPM
PBMC	314.8 nTPM
Breast	244.5 nTPM
Adipose tissue	151.9 nTPM

Endothelial cells	259.5 nTPM
Placenta	412.7 nTPM
Skin	400.9 nTPM
Pancreas	374.5 nTPM
Heart muscle	314.1 nTPM
Breast	292.5 nTPM
Ovary	277.6 nTPM
Testis	266.7 nTPM
Liver	233.0 nTPM
Eye	205.5 nTPM
Prostate	204.5 nTPM
Esophagus	189.6 nTPM
Skeletal muscle	185.6 nTPM
Endometrium	142.0 nTPM
Lung	134.1 nTPM

Enteroendocrine cells	212.4 nTPM
Rectum	233.0 nTPM
Colon	191.9 nTPM

Erythroid cells	220.7 nTPM
Liver	294.3 nTPM
Bone marrow	147.1 nTPM

Fibroblasts	246.0 nTPM
Placenta	403.4 nTPM
Skin	368.0 nTPM
Heart muscle	339.2 nTPM
Breast	254.9 nTPM
Ovary	254.2 nTPM
Adipose tissue	248.2 nTPM
Esophagus	197.8 nTPM
Lung	182.0 nTPM
Prostate	158.9 nTPM
Skeletal muscle	155.6 nTPM
Stomach	144.0 nTPM

Intestinal goblet cells	286.4 nTPM
Colon	408.8 nTPM
Small intestine	233.7 nTPM
Rectum	216.5 nTPM

Macrophages	255.4 nTPM
Kidney	565.7 nTPM
Pancreas	485.0 nTPM
Ovary	284.6 nTPM
Prostate	278.5 nTPM
Testis	266.1 nTPM
Breast	248.8 nTPM
Endometrium	211.5 nTPM
Lung	211.4 nTPM
Bone marrow	211.2 nTPM
Esophagus	207.7 nTPM
Stomach	190.5 nTPM
Adipose tissue	188.2 nTPM
Spleen	184.5 nTPM
Skeletal muscle	161.3 nTPM
PBMC	136.4 nTPM

Paneth cells	311.5 nTPM
Colon	415.0 nTPM
Small intestine	274.0 nTPM
Rectum	245.5 nTPM

Plasma cells	161.3 nTPM
Spleen	274.7 nTPM
Bone marrow	184.5 nTPM
Stomach	161.8 nTPM
Esophagus	117.0 nTPM
Adipose tissue	68.3 nTPM

Cholangiocytes	215.9 nTPM
Liver	215.9 nTPM

Collecting duct cells	310.8 nTPM
Kidney	310.8 nTPM

Cone photoreceptor cells	47.9 nTPM
Eye	47.9 nTPM

Cytotrophoblasts	525.7 nTPM
Placenta	525.7 nTPM

Respiratory ciliated cells	279.7 nTPM
Bronchus	410.7 nTPM
Lung	148.6 nTPM

Smooth muscle cells	318.4 nTPM
Bronchus	617.2 nTPM
Pancreas	594.6 nTPM
Heart muscle	406.1 nTPM
Skin	326.4 nTPM
Breast	304.0 nTPM
Ovary	270.1 nTPM
Esophagus	227.9 nTPM
Prostate	222.9 nTPM
Adipose tissue	198.1 nTPM
Skeletal muscle	195.5 nTPM
Endometrium	139.2 nTPM

T-cells	216.0 nTPM
Kidney	388.8 nTPM
Skin	386.8 nTPM
Liver	299.2 nTPM
Ovary	293.7 nTPM
PBMC	287.1 nTPM
Colon	221.5 nTPM
Breast	214.6 nTPM
Spleen	193.3 nTPM
Skeletal muscle	182.6 nTPM
Stomach	181.3 nTPM
Bone marrow	171.5 nTPM
Lung	164.0 nTPM
Lymph node	153.0 nTPM
Adipose tissue	150.5 nTPM
Endometrium	143.7 nTPM
Prostate	142.0 nTPM
Esophagus	98.3 nTPM

Undifferentiated cells	291.8 nTPM
Colon	376.3 nTPM
Small intestine	253.7 nTPM
Rectum	245.5 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