Single cell type - ATG4B - 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.	ATG4B
Gene descriptionⁱ Full gene name according to HGNC.	Autophagy related 4B cysteine peptidase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes 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.	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	Intestinal epithelial cells - 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

ATG4B is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
GPATCH3	G-patch domain containing 3	0.4958	20
KAT5	Lysine acetyltransferase 5	0.4876	26
BRMS1	BRMS1 transcriptional repressor and anoikis regulator	0.4831	53
RHBDD3	Rhomboid domain containing 3	0.4771	47
ATP6V0D1	ATPase H+ transporting V0 subunit d1	0.4731	4
SIRT7	Sirtuin 7	0.4722	53
B3GALT4	Beta-1,3-galactosyltransferase 4	0.4711	66
SSNA1	SS nuclear autoantigen 1	0.4662	53
CHMP1A	Charged multivesicular body protein 1A	0.4591	53
PPP4C	Protein phosphatase 4 catalytic subunit	0.4564	53
SQLE	Squalene epoxidase	0.4496	26
RTCB	RNA 2',3'-cyclic phosphate and 5'-OH ligase	0.4479	67
ZC3H3	Zinc finger CCCH-type containing 3	0.4446	40
DDX43	DEAD-box helicase 43	0.4443	20
GALNS	Galactosamine (N-acetyl)-6-sulfatase	0.4420	20

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	23.2 nTPM
Adipose tissue	25.7 nTPM
Breast	20.8 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	33.8 nTPM
Lung	33.8 nTPM

Astrocytes	41.1 nTPM
Brain	41.1 nTPM

B-cells	25.6 nTPM
Lymph node	35.4 nTPM
Liver	33.8 nTPM
Colon	33.5 nTPM
Stomach	29.0 nTPM
Spleen	27.3 nTPM
PBMC	25.7 nTPM
Adipose tissue	22.5 nTPM
Breast	20.0 nTPM
Bone marrow	19.6 nTPM
Kidney	9.5 nTPM

Dendritic cells	33.5 nTPM
Adipose tissue	35.4 nTPM
Breast	33.2 nTPM
PBMC	31.8 nTPM

Endothelial cells	25.3 nTPM
Pancreas	38.6 nTPM
Prostate	36.5 nTPM
Ovary	35.1 nTPM
Placenta	33.5 nTPM
Testis	27.9 nTPM
Endometrium	27.6 nTPM
Heart muscle	25.6 nTPM
Skin	25.4 nTPM
Skeletal muscle	25.2 nTPM
Liver	21.1 nTPM
Breast	21.1 nTPM
Esophagus	18.0 nTPM
Eye	14.6 nTPM
Lung	3.1 nTPM

Fibroblasts	22.6 nTPM
Prostate	36.1 nTPM
Placenta	31.2 nTPM
Ovary	30.3 nTPM
Breast	23.4 nTPM
Skin	22.1 nTPM
Esophagus	21.7 nTPM
Skeletal muscle	20.8 nTPM
Adipose tissue	20.1 nTPM
Stomach	17.8 nTPM
Heart muscle	13.4 nTPM
Lung	12.3 nTPM

Intestinal goblet cells	36.4 nTPM
Colon	42.9 nTPM
Rectum	39.2 nTPM
Small intestine	27.1 nTPM

Macrophages	30.7 nTPM
Prostate	42.3 nTPM
Adipose tissue	38.5 nTPM
Pancreas	35.7 nTPM
Esophagus	34.6 nTPM
Testis	34.3 nTPM
Skeletal muscle	33.9 nTPM
Kidney	32.5 nTPM
Lung	32.3 nTPM
Ovary	30.8 nTPM
Endometrium	30.4 nTPM
Breast	30.4 nTPM
Stomach	29.4 nTPM
Spleen	27.9 nTPM
Bone marrow	27.5 nTPM
PBMC	0.0 nTPM

Paneth cells	41.5 nTPM
Colon	65.8 nTPM
Small intestine	30.0 nTPM
Rectum	28.7 nTPM

Plasma cells	28.6 nTPM
Spleen	39.0 nTPM
Adipose tissue	36.7 nTPM
Bone marrow	28.0 nTPM
Stomach	20.6 nTPM
Esophagus	18.4 nTPM

Respiratory ciliated cells	26.7 nTPM
Bronchus	41.6 nTPM
Lung	11.7 nTPM

Smooth muscle cells	22.8 nTPM
Pancreas	40.0 nTPM
Skin	28.9 nTPM
Ovary	26.8 nTPM
Prostate	26.3 nTPM
Endometrium	23.5 nTPM
Skeletal muscle	23.3 nTPM
Breast	18.9 nTPM
Esophagus	18.6 nTPM
Adipose tissue	18.3 nTPM
Heart muscle	14.5 nTPM
Bronchus	11.2 nTPM

T-cells	29.4 nTPM
Ovary	44.5 nTPM
Lung	39.5 nTPM
Colon	39.0 nTPM
Lymph node	35.8 nTPM
Liver	33.9 nTPM
Spleen	30.9 nTPM
Adipose tissue	30.7 nTPM
Stomach	30.0 nTPM
Breast	29.7 nTPM
Endometrium	29.5 nTPM
Bone marrow	28.8 nTPM
Skeletal muscle	28.1 nTPM
Kidney	24.7 nTPM
Skin	24.0 nTPM
PBMC	23.2 nTPM
Prostate	14.2 nTPM
Esophagus	13.1 nTPM

Basal keratinocytes	24.3 nTPM
Skin	24.3 nTPM

Basal prostatic cells	27.2 nTPM
Prostate	27.2 nTPM

Basal respiratory cells	41.3 nTPM
Bronchus	41.3 nTPM

Cholangiocytes	25.8 nTPM
Liver	25.8 nTPM

Undifferentiated cells	35.6 nTPM
Colon	44.6 nTPM
Rectum	34.1 nTPM
Small intestine	28.1 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