Single cell type - NEDD4 - 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.	NEDD4
Gene descriptionⁱ Full gene name according to HGNC.	NEDD4 E3 ubiquitin protein ligase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins Transporters
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	Alveolar cells - Smell perception (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 (Alveolar cells type 2, Alveolar cells type 1, Respiratory ciliated cells, granulocytes, Oligodendrocyte precursor cells)
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	Not detected in immune cells
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	Not detected
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 many
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 (Alveolar cells type 2, Alveolar cells type 1, Respiratory ciliated cells, granulocytes, Oligodendrocyte precursor cells)

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

NEDD4 is part of cluster 11 Alveolar cells - Smell perception with confidenceⁱ 0.9
281 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
OR1A1	Olfactory receptor family 1 subfamily A member 1	0.7178	11
AC104109.3	Novel protein	0.7042	11
OR52I1	Olfactory receptor family 52 subfamily I member 1	0.7004	11
OR6C75	Olfactory receptor family 6 subfamily C member 75	0.6985	11
OR10H1	Olfactory receptor family 10 subfamily H member 1	0.6932	11
OR10K1	Olfactory receptor family 10 subfamily K member 1	0.6816	11
NPIPB13	Nuclear pore complex interacting protein family, member B13	0.6771	11
AC087721.2	Novel protein	0.6698	11
AL355916.3	Novel protein	0.6628	11
OR2G6	Olfactory receptor family 2 subfamily G member 6	0.6560	11
RPL36A-HNRNPH2	RPL36A-HNRNPH2 readthrough	0.6538	11
OR4F17	Olfactory receptor family 4 subfamily F member 17	0.6462	11
AP001267.5	Novel protein	0.6448	11
TBC1D8B	TBC1 domain family member 8B	0.6426	11
TMEM35B	Transmembrane protein 35B	0.6402	11

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	35.9 nTPM
Adipose tissue	42.2 nTPM
Breast	29.6 nTPM

Astrocytes	28.4 nTPM
Brain	28.4 nTPM

B-cells	1.6 nTPM
Kidney	4.8 nTPM
Colon	3.2 nTPM
Stomach	2.2 nTPM
Liver	1.7 nTPM
Spleen	1.4 nTPM
Breast	1.3 nTPM
Lymph node	1.1 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM

Basal keratinocytes	12.1 nTPM
Skin	12.1 nTPM

Basal prostatic cells	3.4 nTPM
Prostate	3.4 nTPM

Dendritic cells	2.0 nTPM
Breast	4.0 nTPM
Adipose tissue	2.0 nTPM
PBMC	0.0 nTPM

Endothelial cells	31.1 nTPM
Lung	127.9 nTPM
Heart muscle	51.2 nTPM
Ovary	39.7 nTPM
Endometrium	32.4 nTPM
Skeletal muscle	30.3 nTPM
Esophagus	24.3 nTPM
Testis	22.0 nTPM
Prostate	19.5 nTPM
Breast	18.5 nTPM
Liver	17.4 nTPM
Pancreas	15.5 nTPM
Placenta	13.7 nTPM
Eye	12.9 nTPM
Skin	10.2 nTPM

Fibroblasts	18.5 nTPM
Lung	108.4 nTPM
Skeletal muscle	14.1 nTPM
Adipose tissue	13.5 nTPM
Esophagus	12.3 nTPM
Stomach	10.4 nTPM
Breast	9.0 nTPM
Heart muscle	8.6 nTPM
Ovary	8.0 nTPM
Placenta	7.9 nTPM
Skin	6.0 nTPM
Prostate	5.5 nTPM

Intestinal goblet cells	4.0 nTPM
Small intestine	5.7 nTPM
Rectum	4.9 nTPM
Colon	1.4 nTPM

Macrophages	8.8 nTPM
Lung	77.3 nTPM
Prostate	6.9 nTPM
Skeletal muscle	6.6 nTPM
Bone marrow	6.2 nTPM
Stomach	5.9 nTPM
Pancreas	5.1 nTPM
Adipose tissue	5.1 nTPM
Endometrium	4.1 nTPM
Breast	3.4 nTPM
Spleen	3.1 nTPM
Kidney	3.0 nTPM
Ovary	2.4 nTPM
Esophagus	1.6 nTPM
Testis	0.6 nTPM
PBMC	0.0 nTPM

Paneth cells	0.8 nTPM
Rectum	2.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	1.9 nTPM
Esophagus	6.1 nTPM
Adipose tissue	1.3 nTPM
Spleen	1.0 nTPM
Stomach	1.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	75.5 nTPM
Lung	147.2 nTPM
Bronchus	3.8 nTPM

Smooth muscle cells	17.7 nTPM
Bronchus	91.6 nTPM
Heart muscle	22.1 nTPM
Endometrium	16.4 nTPM
Breast	12.2 nTPM
Pancreas	10.2 nTPM
Esophagus	9.3 nTPM
Adipose tissue	8.3 nTPM
Ovary	7.4 nTPM
Skeletal muscle	7.3 nTPM
Skin	5.2 nTPM
Prostate	5.0 nTPM

T-cells	9.4 nTPM
Lung	89.6 nTPM
Stomach	9.4 nTPM
Ovary	8.9 nTPM
Esophagus	6.6 nTPM
Adipose tissue	5.9 nTPM
Spleen	5.3 nTPM
Skeletal muscle	4.7 nTPM
Breast	4.6 nTPM
Lymph node	4.5 nTPM
Endometrium	4.1 nTPM
Bone marrow	3.7 nTPM
Kidney	2.7 nTPM
Liver	2.5 nTPM
PBMC	2.5 nTPM
Colon	2.4 nTPM
Skin	1.9 nTPM
Prostate	0.0 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Cone photoreceptor cells	22.9 nTPM
Eye	22.9 nTPM

Cytotrophoblasts	23.2 nTPM
Placenta	23.2 nTPM

Endometrial stromal cells	13.3 nTPM
Endometrium	13.3 nTPM

Undifferentiated cells	5.6 nTPM
Small intestine	11.4 nTPM
Colon	2.8 nTPM
Rectum	2.6 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