Single cell type - HELLS - 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.	HELLS
Gene descriptionⁱ Full gene name according to HGNC.	Helicase, lymphoid specific
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease related genes
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.	8

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 - Cell cycle regulation (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 (Spermatocytes, Spermatogonia)
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	Immune cell enhanced (plasmacytoid DC)
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 many
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 (Spermatocytes, Spermatogonia)

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

HELLS is part of cluster 12 Non-specific - Cell cycle regulation with confidenceⁱ 1
294 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
ORC6	Origin recognition complex subunit 6	0.7865	12
BRCA1	BRCA1 DNA repair associated	0.7620	12
CHEK1	Checkpoint kinase 1	0.7601	12
GINS2	GINS complex subunit 2	0.7594	12
FANCA	FA complementation group A	0.7369	12
CDC6	Cell division cycle 6	0.7322	12
ESCO2	Establishment of sister chromatid cohesion N-acetyltransferase 2	0.7204	12
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	0.7202	12
TOP2A	DNA topoisomerase II alpha	0.7138	12
FBXO5	F-box protein 5	0.7085	12
FANCI	FA complementation group I	0.7058	12
RECQL4	RecQ like helicase 4	0.6975	12
FANCD2	FA complementation group D2	0.6951	12
CENPK	Centromere protein K	0.6933	12
CLSPN	Claspin	0.6908	13

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	4.7 nTPM
Adipose tissue	5.4 nTPM
Breast	3.9 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	3.9 nTPM
Lung	3.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	19.7 nTPM
Liver	57.2 nTPM
Colon	27.1 nTPM
Adipose tissue	24.6 nTPM
Kidney	23.8 nTPM
Bone marrow	12.3 nTPM
PBMC	11.5 nTPM
Breast	10.7 nTPM
Stomach	10.5 nTPM
Lymph node	9.9 nTPM
Spleen	9.0 nTPM

Dendritic cells	13.2 nTPM
Adipose tissue	18.3 nTPM
PBMC	12.0 nTPM
Breast	9.1 nTPM

Endothelial cells	8.1 nTPM
Endometrium	20.3 nTPM
Placenta	19.9 nTPM
Ovary	17.1 nTPM
Skin	9.0 nTPM
Liver	7.3 nTPM
Testis	6.2 nTPM
Eye	5.7 nTPM
Skeletal muscle	5.3 nTPM
Breast	5.1 nTPM
Prostate	4.8 nTPM
Pancreas	3.9 nTPM
Heart muscle	3.1 nTPM
Lung	3.1 nTPM
Esophagus	3.1 nTPM

Fibroblasts	13.0 nTPM
Ovary	61.3 nTPM
Placenta	16.6 nTPM
Lung	13.4 nTPM
Prostate	12.4 nTPM
Skin	11.8 nTPM
Esophagus	6.2 nTPM
Skeletal muscle	6.0 nTPM
Breast	5.3 nTPM
Heart muscle	4.0 nTPM
Adipose tissue	3.2 nTPM
Stomach	3.0 nTPM

Intestinal goblet cells	17.8 nTPM
Colon	24.3 nTPM
Small intestine	23.1 nTPM
Rectum	5.9 nTPM

Macrophages	7.3 nTPM
Esophagus	18.9 nTPM
Endometrium	18.8 nTPM
Breast	11.0 nTPM
Bone marrow	10.0 nTPM
Lung	7.8 nTPM
Pancreas	7.7 nTPM
Adipose tissue	7.2 nTPM
Prostate	6.9 nTPM
Skeletal muscle	6.9 nTPM
Spleen	5.2 nTPM
Testis	4.0 nTPM
Kidney	3.8 nTPM
Ovary	1.5 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.8 nTPM
Rectum	5.5 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	37.5 nTPM
Spleen	81.9 nTPM
Bone marrow	69.2 nTPM
Adipose tissue	22.5 nTPM
Stomach	14.0 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	6.3 nTPM
Lung	8.7 nTPM
Bronchus	3.9 nTPM

Smooth muscle cells	16.4 nTPM
Bronchus	63.5 nTPM
Endometrium	37.2 nTPM
Pancreas	21.7 nTPM
Ovary	19.4 nTPM
Heart muscle	8.2 nTPM
Skin	6.0 nTPM
Breast	5.8 nTPM
Prostate	5.3 nTPM
Skeletal muscle	5.3 nTPM
Adipose tissue	5.0 nTPM
Esophagus	3.1 nTPM

T-cells	15.7 nTPM
Lung	33.4 nTPM
Endometrium	27.7 nTPM
Colon	27.1 nTPM
Esophagus	26.2 nTPM
Adipose tissue	22.0 nTPM
Skeletal muscle	18.9 nTPM
Skin	15.2 nTPM
Liver	13.9 nTPM
Bone marrow	12.9 nTPM
Kidney	12.3 nTPM
Breast	11.7 nTPM
Ovary	11.1 nTPM
PBMC	10.6 nTPM
Spleen	10.1 nTPM
Lymph node	7.3 nTPM
Stomach	5.7 nTPM
Prostate	0.0 nTPM

Basal keratinocytes	21.5 nTPM
Skin	21.5 nTPM

Basal respiratory cells	12.6 nTPM
Bronchus	12.6 nTPM

Basal squamous epithelial cells	13.1 nTPM
Esophagus	13.1 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Undifferentiated cells	30.9 nTPM
Small intestine	43.4 nTPM
Colon	33.2 nTPM
Rectum	16.2 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