Single cell type - HERC1 - 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.	HERC1
Gene descriptionⁱ Full gene name according to HGNC.	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	6

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	Neurons & Oligodendrocytes - Neuronal signaling (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 (Excitatory neurons, Inhibitory neurons, Oligodendrocytes)
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: Cell type enhanced (Excitatory neurons, Inhibitory neurons, Oligodendrocytes)

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

HERC1 is part of cluster 21 Neurons & Oligodendrocytes - Neuronal signaling with confidenceⁱ 1
589 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
ASIC2	Acid sensing ion channel subunit 2	0.8202	21
AGBL4	ATP/GTP binding protein like 4	0.8185	21
PTPRD	Protein tyrosine phosphatase receptor type D	0.8072	21
KCNMB4	Potassium calcium-activated channel subfamily M regulatory beta subunit 4	0.8009	21
ERC2	ELKS/RAB6-interacting/CAST family member 2	0.7871	21
TMEM178A	Transmembrane protein 178A	0.7828	21
OLFM3	Olfactomedin 3	0.7786	21
ADAMTSL1	ADAMTS like 1	0.7691	21
HS3ST2	Heparan sulfate-glucosamine 3-sulfotransferase 2	0.7637	21
BTNL2	Butyrophilin like 2	0.7446	21
RFPL2	Ret finger protein like 2	0.7424	21
OR52N4	Olfactory receptor family 52 subfamily N member 4	0.7383	21
OR2AG2	Olfactory receptor family 2 subfamily AG member 2	0.7383	21
CALHM1	Calcium homeostasis modulator 1	0.7379	21
ZNF385B	Zinc finger protein 385B	0.7376	21

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	66.0 nTPM
Adipose tissue	70.5 nTPM
Breast	61.5 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	39.5 nTPM
Lung	39.5 nTPM

Astrocytes	113.0 nTPM
Brain	113.0 nTPM

B-cells	44.2 nTPM
Adipose tissue	73.1 nTPM
Bone marrow	62.1 nTPM
Lymph node	50.8 nTPM
Stomach	49.1 nTPM
Breast	48.1 nTPM
Spleen	46.4 nTPM
Colon	28.7 nTPM
Kidney	28.5 nTPM
Liver	27.8 nTPM
PBMC	27.1 nTPM

Dendritic cells	66.1 nTPM
PBMC	67.8 nTPM
Adipose tissue	67.4 nTPM
Breast	63.1 nTPM

Endothelial cells	44.5 nTPM
Ovary	112.4 nTPM
Heart muscle	106.4 nTPM
Skeletal muscle	55.1 nTPM
Liver	40.3 nTPM
Breast	38.4 nTPM
Eye	37.2 nTPM
Endometrium	35.1 nTPM
Skin	31.8 nTPM
Esophagus	30.5 nTPM
Testis	28.2 nTPM
Lung	28.1 nTPM
Placenta	27.8 nTPM
Pancreas	27.0 nTPM
Prostate	24.6 nTPM

Fibroblasts	28.5 nTPM
Heart muscle	45.7 nTPM
Stomach	41.6 nTPM
Ovary	40.3 nTPM
Skeletal muscle	30.9 nTPM
Breast	29.4 nTPM
Adipose tissue	26.2 nTPM
Prostate	24.2 nTPM
Esophagus	24.0 nTPM
Skin	20.9 nTPM
Lung	19.0 nTPM
Placenta	11.3 nTPM

Intestinal goblet cells	13.1 nTPM
Rectum	17.2 nTPM
Small intestine	12.7 nTPM
Colon	9.3 nTPM

Macrophages	39.2 nTPM
Spleen	61.1 nTPM
Bone marrow	60.0 nTPM
Esophagus	55.1 nTPM
Breast	54.9 nTPM
Adipose tissue	54.8 nTPM
Ovary	49.8 nTPM
Skeletal muscle	44.3 nTPM
Stomach	43.9 nTPM
Endometrium	39.3 nTPM
Lung	31.0 nTPM
Testis	23.8 nTPM
Prostate	22.9 nTPM
Kidney	21.1 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM

Paneth cells	14.7 nTPM
Small intestine	22.5 nTPM
Rectum	15.0 nTPM
Colon	6.5 nTPM

Plasma cells	44.9 nTPM
Adipose tissue	112.9 nTPM
Bone marrow	34.6 nTPM
Spleen	30.5 nTPM
Esophagus	24.6 nTPM
Stomach	22.1 nTPM

Respiratory ciliated cells	16.6 nTPM
Lung	20.4 nTPM
Bronchus	12.7 nTPM

Smooth muscle cells	36.0 nTPM
Adipose tissue	64.7 nTPM
Heart muscle	51.7 nTPM
Skeletal muscle	47.7 nTPM
Bronchus	47.4 nTPM
Ovary	46.1 nTPM
Breast	34.8 nTPM
Endometrium	33.2 nTPM
Skin	21.3 nTPM
Prostate	20.0 nTPM
Esophagus	17.0 nTPM
Pancreas	12.3 nTPM

T-cells	61.1 nTPM
Adipose tissue	117.4 nTPM
Endometrium	101.7 nTPM
Skeletal muscle	90.8 nTPM
Breast	88.6 nTPM
Stomach	80.4 nTPM
Ovary	69.0 nTPM
Spleen	62.9 nTPM
Bone marrow	62.8 nTPM
Lymph node	60.9 nTPM
Colon	57.0 nTPM
PBMC	50.3 nTPM
Liver	42.5 nTPM
Lung	38.0 nTPM
Prostate	37.9 nTPM
Skin	36.8 nTPM
Kidney	22.6 nTPM
Esophagus	19.7 nTPM

Basal keratinocytes	14.9 nTPM
Skin	14.9 nTPM

Basal prostatic cells	10.6 nTPM
Prostate	10.6 nTPM

Basal respiratory cells	16.1 nTPM
Bronchus	16.1 nTPM

Basal squamous epithelial cells	17.1 nTPM
Esophagus	17.1 nTPM

Undifferentiated cells	14.4 nTPM
Rectum	17.4 nTPM
Small intestine	13.5 nTPM
Colon	12.3 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