Single cell type - ATG4A - 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.	ATG4A
Gene descriptionⁱ Full gene name according to HGNC.	Autophagy related 4A cysteine peptidase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	4

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	Erythroid cells - Oxygen transport (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	Cell line enhanced (HUVEC TERT2)
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

ATG4A is part of cluster 6 Erythroid cells - Oxygen transport with confidenceⁱ 1
151 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
BPGM	Bisphosphoglycerate mutase	0.6028	6
C9orf78	Chromosome 9 open reading frame 78	0.5639	6
FAM117A	Family with sequence similarity 117 member A	0.5596	6
PRDX2	Peroxiredoxin 2	0.5448	6
STRADB	STE20 related adaptor beta	0.5307	6
TCEANC	Transcription elongation factor A N-terminal and central domain containing	0.5273	6
SMIM1	Small integral membrane protein 1 (Vel blood group)	0.5271	6
CMPK2	Cytidine/uridine monophosphate kinase 2	0.5205	6
TBCEL	Tubulin folding cofactor E like	0.5086	6
SLC25A39	Solute carrier family 25 member 39	0.4975	6
UROD	Uroporphyrinogen decarboxylase	0.4934	6
ST6GALNAC4	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	0.4862	6
FECH	Ferrochelatase	0.4839	6
CISD2	CDGSH iron sulfur domain 2	0.4719	6
UBR2	Ubiquitin protein ligase E3 component n-recognin 2	0.4713	6

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	13.6 nTPM
Breast	18.0 nTPM
Adipose tissue	9.2 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	10.3 nTPM
Lung	10.3 nTPM

Astrocytes	9.1 nTPM
Brain	9.1 nTPM

B-cells	8.1 nTPM
Breast	22.8 nTPM
Liver	14.6 nTPM
Kidney	9.5 nTPM
Spleen	7.2 nTPM
Lymph node	6.3 nTPM
Stomach	5.4 nTPM
Bone marrow	4.9 nTPM
PBMC	4.3 nTPM
Adipose tissue	4.0 nTPM
Colon	1.6 nTPM

Dendritic cells	12.4 nTPM
Breast	22.6 nTPM
Adipose tissue	10.8 nTPM
PBMC	4.0 nTPM

Endothelial cells	12.9 nTPM
Ovary	32.3 nTPM
Pancreas	27.0 nTPM
Testis	14.9 nTPM
Heart muscle	14.6 nTPM
Eye	13.7 nTPM
Placenta	12.5 nTPM
Esophagus	11.9 nTPM
Skeletal muscle	11.2 nTPM
Breast	9.8 nTPM
Endometrium	8.5 nTPM
Prostate	8.2 nTPM
Lung	6.2 nTPM
Skin	5.7 nTPM
Liver	3.7 nTPM

Fibroblasts	4.6 nTPM
Heart muscle	6.5 nTPM
Placenta	6.3 nTPM
Skeletal muscle	6.2 nTPM
Breast	5.7 nTPM
Adipose tissue	5.4 nTPM
Skin	5.0 nTPM
Esophagus	5.0 nTPM
Stomach	4.4 nTPM
Ovary	3.4 nTPM
Prostate	1.5 nTPM
Lung	1.2 nTPM

Intestinal goblet cells	9.0 nTPM
Colon	12.9 nTPM
Rectum	7.8 nTPM
Small intestine	6.4 nTPM

Macrophages	7.3 nTPM
Lung	14.3 nTPM
Testis	11.1 nTPM
Ovary	11.0 nTPM
Breast	10.4 nTPM
Kidney	9.1 nTPM
Skeletal muscle	8.9 nTPM
Endometrium	7.5 nTPM
Spleen	7.2 nTPM
Adipose tissue	6.8 nTPM
Esophagus	6.3 nTPM
Stomach	5.9 nTPM
Prostate	4.6 nTPM
Bone marrow	3.7 nTPM
Pancreas	2.5 nTPM
PBMC	0.0 nTPM

Paneth cells	8.0 nTPM
Small intestine	11.3 nTPM
Colon	6.5 nTPM
Rectum	6.1 nTPM

Plasma cells	23.5 nTPM
Stomach	41.3 nTPM
Esophagus	30.7 nTPM
Spleen	26.1 nTPM
Bone marrow	9.9 nTPM
Adipose tissue	9.7 nTPM

Respiratory ciliated cells	17.2 nTPM
Lung	19.0 nTPM
Bronchus	15.4 nTPM

Smooth muscle cells	6.9 nTPM
Pancreas	10.2 nTPM
Prostate	9.1 nTPM
Heart muscle	8.9 nTPM
Breast	8.5 nTPM
Bronchus	7.4 nTPM
Skin	5.9 nTPM
Endometrium	5.9 nTPM
Skeletal muscle	5.5 nTPM
Adipose tissue	5.2 nTPM
Esophagus	4.6 nTPM
Ovary	4.1 nTPM

T-cells	12.0 nTPM
Prostate	23.6 nTPM
Lung	19.7 nTPM
Ovary	15.6 nTPM
Breast	14.8 nTPM
Colon	13.8 nTPM
Liver	13.2 nTPM
Esophagus	13.1 nTPM
Stomach	11.9 nTPM
Spleen	10.8 nTPM
Skin	10.5 nTPM
Adipose tissue	9.6 nTPM
PBMC	9.0 nTPM
Bone marrow	8.7 nTPM
Kidney	8.2 nTPM
Endometrium	7.8 nTPM
Lymph node	7.5 nTPM
Skeletal muscle	6.5 nTPM

Basal keratinocytes	5.1 nTPM
Skin	5.1 nTPM

Basal respiratory cells	13.5 nTPM
Bronchus	13.5 nTPM

Basal squamous epithelial cells	2.8 nTPM
Esophagus	2.8 nTPM

Cone photoreceptor cells	4.2 nTPM
Eye	4.2 nTPM

Undifferentiated cells	5.6 nTPM
Colon	6.5 nTPM
Rectum	5.3 nTPM
Small intestine	4.9 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