Single cell type - DDX56 - 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.	DDX56
Gene descriptionⁱ Full gene name according to HGNC.	DEAD-box helicase 56
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.	3

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 - Basic cellular processes (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

DDX56 is part of cluster 39 Non-specific - Basic cellular processes with confidenceⁱ 0.99
586 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
FAHD1	Fumarylacetoacetate hydrolase domain containing 1	0.5784	67
WDR18	WD repeat domain 18	0.5417	67
TRMU	TRNA mitochondrial 2-thiouridylase	0.5134	52
ECHDC1	Ethylmalonyl-CoA decarboxylase 1	0.5119	67
ABCF3	ATP binding cassette subfamily F member 3	0.5083	39
TMEM161A	Transmembrane protein 161A	0.5082	39
LONP1	Lon peptidase 1, mitochondrial	0.5037	39
GADD45GIP1	GADD45G interacting protein 1	0.4930	39
WDR46	WD repeat domain 46	0.4928	39
PMPCA	Peptidase, mitochondrial processing subunit alpha	0.4915	47
FARSA	Phenylalanyl-tRNA synthetase subunit alpha	0.4849	39
TRAP1	TNF receptor associated protein 1	0.4831	67
RRP1	Ribosomal RNA processing 1	0.4807	39
PES1	Pescadillo ribosomal biogenesis factor 1	0.4719	39
SAMM50	SAMM50 sorting and assembly machinery component	0.4701	39

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	21.5 nTPM
Breast	22.4 nTPM
Adipose tissue	20.7 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	29.0 nTPM
Lung	29.0 nTPM

Astrocytes	13.1 nTPM
Brain	13.1 nTPM

B-cells	22.8 nTPM
Stomach	33.2 nTPM
Bone marrow	32.7 nTPM
Spleen	29.4 nTPM
Breast	25.5 nTPM
Liver	24.8 nTPM
Adipose tissue	21.6 nTPM
Colon	19.2 nTPM
Lymph node	18.0 nTPM
PBMC	14.3 nTPM
Kidney	9.5 nTPM

Dendritic cells	19.1 nTPM
Breast	28.1 nTPM
Adipose tissue	21.3 nTPM
PBMC	8.0 nTPM

Endothelial cells	26.4 nTPM
Pancreas	50.2 nTPM
Placenta	39.3 nTPM
Heart muscle	36.7 nTPM
Ovary	28.9 nTPM
Lung	28.1 nTPM
Prostate	27.6 nTPM
Eye	25.1 nTPM
Testis	22.5 nTPM
Endometrium	20.4 nTPM
Skeletal muscle	20.4 nTPM
Esophagus	20.0 nTPM
Breast	19.2 nTPM
Skin	17.0 nTPM
Liver	14.7 nTPM

Fibroblasts	24.6 nTPM
Lung	44.6 nTPM
Placenta	39.9 nTPM
Ovary	35.4 nTPM
Stomach	23.7 nTPM
Prostate	20.9 nTPM
Adipose tissue	20.9 nTPM
Skeletal muscle	20.2 nTPM
Breast	20.1 nTPM
Esophagus	19.6 nTPM
Skin	17.3 nTPM
Heart muscle	8.3 nTPM

Intestinal goblet cells	24.9 nTPM
Colon	32.2 nTPM
Rectum	22.0 nTPM
Small intestine	20.7 nTPM

Macrophages	17.9 nTPM
Kidney	28.7 nTPM
Breast	23.2 nTPM
Lung	22.2 nTPM
Endometrium	22.2 nTPM
Esophagus	22.0 nTPM
Pancreas	20.4 nTPM
Ovary	19.0 nTPM
Skeletal muscle	18.6 nTPM
Spleen	18.6 nTPM
Bone marrow	17.5 nTPM
Adipose tissue	15.9 nTPM
Stomach	14.7 nTPM
Prostate	13.8 nTPM
Testis	11.7 nTPM
PBMC	0.0 nTPM

Paneth cells	18.8 nTPM
Rectum	25.6 nTPM
Colon	23.1 nTPM
Small intestine	7.5 nTPM

Plasma cells	18.2 nTPM
Adipose tissue	26.4 nTPM
Stomach	25.9 nTPM
Spleen	23.7 nTPM
Bone marrow	14.8 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	31.8 nTPM
Bronchus	37.4 nTPM
Lung	26.2 nTPM

Smooth muscle cells	25.1 nTPM
Pancreas	59.0 nTPM
Heart muscle	32.4 nTPM
Ovary	30.9 nTPM
Skeletal muscle	21.9 nTPM
Prostate	21.3 nTPM
Bronchus	20.7 nTPM
Breast	20.5 nTPM
Endometrium	20.3 nTPM
Esophagus	20.1 nTPM
Adipose tissue	14.7 nTPM
Skin	14.2 nTPM

T-cells	23.6 nTPM
Lung	38.0 nTPM
Kidney	34.2 nTPM
Ovary	31.1 nTPM
Breast	29.6 nTPM
Stomach	29.4 nTPM
PBMC	27.2 nTPM
Colon	27.1 nTPM
Bone marrow	26.6 nTPM
Spleen	23.7 nTPM
Skin	20.7 nTPM
Adipose tissue	19.8 nTPM
Skeletal muscle	19.4 nTPM
Prostate	19.0 nTPM
Endometrium	19.0 nTPM
Liver	18.9 nTPM
Lymph node	17.6 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	17.1 nTPM
Skin	17.1 nTPM

Basal prostatic cells	23.9 nTPM
Prostate	23.9 nTPM

Basal respiratory cells	45.1 nTPM
Bronchus	45.1 nTPM

Basal squamous epithelial cells	21.1 nTPM
Esophagus	21.1 nTPM

Undifferentiated cells	36.8 nTPM
Colon	51.6 nTPM
Small intestine	30.4 nTPM
Rectum	28.3 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