Single cell type - ATG4D - 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.	ATG4D
Gene descriptionⁱ Full gene name according to HGNC.	Autophagy related 4D 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	Cell type enhanced (Proximal enterocytes, Distal enterocytes, Spermatocytes)
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 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	Cell line enhanced (NB-4)
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 (Proximal enterocytes, Distal enterocytes, Spermatocytes)

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

ATG4D 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
ACOT8	Acyl-CoA thioesterase 8	0.7133	53
SLC22A18	Solute carrier family 22 member 18	0.6221	45
MOGAT3	Monoacylglycerol O-acyltransferase 3	0.6090	53
PPP1R14D	Protein phosphatase 1 regulatory inhibitor subunit 14D	0.6030	53
PDZD3	PDZ domain containing 3	0.5990	53
MISP	Mitotic spindle positioning	0.5925	53
SLC51B	Solute carrier family 51 subunit beta	0.5875	45
EPS8L3	EPS8 like 3	0.5814	53
MPI	Mannose phosphate isomerase	0.5786	45
ACADS	Acyl-CoA dehydrogenase short chain	0.5717	45
AGPAT2	1-acylglycerol-3-phosphate O-acyltransferase 2	0.5713	45
KRT20	Keratin 20	0.5655	53
SULT1A2	Sulfotransferase family 1A member 2	0.5550	45
IL22RA1	Interleukin 22 receptor subunit alpha 1	0.5531	53
C11orf86	Chromosome 11 open reading frame 86	0.5513	45

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	6.3 nTPM
Adipose tissue	6.4 nTPM
Breast	6.2 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	6.6 nTPM
Lung	6.6 nTPM

Astrocytes	9.1 nTPM
Brain	9.1 nTPM

B-cells	14.4 nTPM
Colon	19.2 nTPM
Stomach	19.1 nTPM
Spleen	17.3 nTPM
Lymph node	17.2 nTPM
Bone marrow	16.4 nTPM
Liver	14.3 nTPM
Breast	13.4 nTPM
Adipose tissue	10.5 nTPM
Kidney	9.5 nTPM
PBMC	7.1 nTPM

Dendritic cells	38.7 nTPM
PBMC	43.8 nTPM
Adipose tissue	36.9 nTPM
Breast	35.3 nTPM

Endothelial cells	5.3 nTPM
Prostate	10.1 nTPM
Eye	8.9 nTPM
Skeletal muscle	8.2 nTPM
Skin	7.6 nTPM
Esophagus	7.3 nTPM
Ovary	6.6 nTPM
Breast	6.3 nTPM
Testis	4.4 nTPM
Endometrium	4.1 nTPM
Liver	3.7 nTPM
Placenta	3.4 nTPM
Lung	3.1 nTPM
Heart muscle	1.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	8.2 nTPM
Placenta	16.2 nTPM
Prostate	11.2 nTPM
Skin	11.2 nTPM
Esophagus	8.9 nTPM
Stomach	8.9 nTPM
Ovary	8.3 nTPM
Breast	7.5 nTPM
Adipose tissue	7.0 nTPM
Skeletal muscle	6.7 nTPM
Lung	3.4 nTPM
Heart muscle	0.5 nTPM

Intestinal goblet cells	38.5 nTPM
Colon	57.9 nTPM
Small intestine	30.8 nTPM
Rectum	26.8 nTPM

Macrophages	10.0 nTPM
Pancreas	30.7 nTPM
Prostate	18.4 nTPM
Spleen	12.5 nTPM
Ovary	11.5 nTPM
Adipose tissue	11.1 nTPM
Kidney	10.6 nTPM
Breast	10.1 nTPM
Testis	8.8 nTPM
Skeletal muscle	8.7 nTPM
Esophagus	7.9 nTPM
Bone marrow	7.5 nTPM
Endometrium	5.8 nTPM
Lung	3.2 nTPM
Stomach	2.9 nTPM
PBMC	0.0 nTPM

Paneth cells	72.4 nTPM
Colon	145.0 nTPM
Rectum	42.1 nTPM
Small intestine	30.0 nTPM

Plasma cells	17.6 nTPM
Adipose tissue	32.2 nTPM
Spleen	16.6 nTPM
Stomach	15.6 nTPM
Esophagus	12.3 nTPM
Bone marrow	11.5 nTPM

Respiratory ciliated cells	5.2 nTPM
Bronchus	7.5 nTPM
Lung	2.9 nTPM

Smooth muscle cells	14.2 nTPM
Ovary	21.5 nTPM
Prostate	20.0 nTPM
Skin	19.8 nTPM
Pancreas	18.5 nTPM
Bronchus	17.1 nTPM
Esophagus	17.0 nTPM
Skeletal muscle	13.0 nTPM
Adipose tissue	11.2 nTPM
Endometrium	8.9 nTPM
Breast	8.6 nTPM
Heart muscle	0.4 nTPM

T-cells	19.6 nTPM
Spleen	33.7 nTPM
Bone marrow	30.1 nTPM
Liver	26.8 nTPM
Kidney	26.7 nTPM
Colon	24.2 nTPM
Stomach	22.9 nTPM
Ovary	22.3 nTPM
Skin	22.1 nTPM
Breast	20.5 nTPM
Adipose tissue	19.4 nTPM
Skeletal muscle	17.9 nTPM
Lymph node	17.7 nTPM
PBMC	13.8 nTPM
Endometrium	13.4 nTPM
Lung	12.2 nTPM
Prostate	9.5 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	30.5 nTPM
Skin	30.5 nTPM

Basal respiratory cells	14.9 nTPM
Bronchus	14.9 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Cone photoreceptor cells	14.6 nTPM
Eye	14.6 nTPM

Undifferentiated cells	33.2 nTPM
Colon	46.2 nTPM
Rectum	29.4 nTPM
Small intestine	24.0 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