Single cell type - RNASE4 - 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.	RNASE4
Gene descriptionⁱ Full gene name according to HGNC.	Ribonuclease A family member 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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	Secreted
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	Mucus-secreting cells - Mucin production (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 (Intestinal goblet cells, Enteroendocrine cells, Hepatocytes, Gastric mucus-secreting cells)
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 (classical monocyte)
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 (ASC diff, ASC TERT1, Hep G2, HSkMC, OE19)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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 (Intestinal goblet cells, Enteroendocrine cells, Hepatocytes, Gastric mucus-secreting cells)

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

RNASE4 is part of cluster 27 Mucus-secreting cells - Mucin production with confidenceⁱ 1
121 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
TFF3	Trefoil factor 3	0.7411	27
HEPACAM2	HEPACAM family member 2	0.7312	27
ITLN1	Intelectin 1	0.7231	27
ATOH1	Atonal bHLH transcription factor 1	0.7192	27
ZG16	Zymogen granule protein 16	0.7126	27
REP15	RAB15 effector protein	0.7100	27
FCGBP	Fc fragment of IgG binding protein	0.7088	27
CLCA1	Chloride channel accessory 1	0.7046	27
LRRC31	Leucine rich repeat containing 31	0.7037	27
LRRC26	Leucine rich repeat containing 26	0.7022	27
SPINK4	Serine peptidase inhibitor Kazal type 4	0.7000	27
REG4	Regenerating family member 4	0.6988	27
KLK1	Kallikrein 1	0.6987	27
FOXA3	Forkhead box A3	0.6985	27
BEST2	Bestrophin 2	0.6966	27

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	1.8 nTPM
Adipose tissue	2.2 nTPM
Breast	1.3 nTPM

Alveolar cells type 1	38.5 nTPM
Lung	38.5 nTPM

Alveolar cells type 2	19.1 nTPM
Lung	19.1 nTPM

Astrocytes	2.0 nTPM
Brain	2.0 nTPM

B-cells	3.4 nTPM
Stomach	8.6 nTPM
Colon	4.8 nTPM
Kidney	4.8 nTPM
Lymph node	4.5 nTPM
Liver	2.9 nTPM
Bone marrow	2.5 nTPM
Spleen	2.4 nTPM
PBMC	1.4 nTPM
Breast	1.3 nTPM
Adipose tissue	0.5 nTPM

Dendritic cells	0.3 nTPM
Breast	0.7 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Endothelial cells	4.0 nTPM
Esophagus	16.2 nTPM
Lung	15.6 nTPM
Pancreas	7.7 nTPM
Liver	3.7 nTPM
Breast	3.6 nTPM
Skin	3.0 nTPM
Skeletal muscle	1.6 nTPM
Testis	1.4 nTPM
Placenta	1.1 nTPM
Eye	0.8 nTPM
Prostate	0.5 nTPM
Ovary	0.3 nTPM
Endometrium	0.2 nTPM
Heart muscle	0.1 nTPM

Fibroblasts	39.2 nTPM
Esophagus	174.7 nTPM
Stomach	145.5 nTPM
Adipose tissue	38.8 nTPM
Breast	20.9 nTPM
Skin	20.8 nTPM
Lung	13.4 nTPM
Skeletal muscle	9.1 nTPM
Prostate	5.5 nTPM
Placenta	1.6 nTPM
Heart muscle	1.2 nTPM
Ovary	0.2 nTPM

Intestinal goblet cells	110.0 nTPM
Rectum	120.3 nTPM
Small intestine	107.4 nTPM
Colon	102.2 nTPM

Macrophages	3.6 nTPM
Stomach	11.7 nTPM
Esophagus	11.0 nTPM
Testis	8.8 nTPM
Bone marrow	6.2 nTPM
Spleen	5.2 nTPM
Lung	3.7 nTPM
Pancreas	2.5 nTPM
Adipose tissue	1.7 nTPM
Skeletal muscle	1.2 nTPM
Breast	1.0 nTPM
Kidney	0.8 nTPM
Ovary	0.1 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Endometrium	0.0 nTPM

Paneth cells	33.2 nTPM
Rectum	74.6 nTPM
Small intestine	15.0 nTPM
Colon	9.9 nTPM

Plasma cells	5.9 nTPM
Esophagus	12.3 nTPM
Stomach	11.7 nTPM
Spleen	3.7 nTPM
Bone marrow	1.7 nTPM
Adipose tissue	0.0 nTPM

Respiratory ciliated cells	11.6 nTPM
Lung	17.5 nTPM
Bronchus	5.7 nTPM

Smooth muscle cells	8.1 nTPM
Esophagus	40.3 nTPM
Pancreas	15.7 nTPM
Adipose tissue	11.2 nTPM
Skin	8.3 nTPM
Breast	4.8 nTPM
Prostate	3.2 nTPM
Skeletal muscle	1.6 nTPM
Heart muscle	1.1 nTPM
Bronchus	1.0 nTPM
Endometrium	1.0 nTPM
Ovary	0.6 nTPM

T-cells	0.8 nTPM
Liver	2.0 nTPM
Skin	1.9 nTPM
Lymph node	1.7 nTPM
Bone marrow	1.6 nTPM
Lung	1.5 nTPM
Colon	1.4 nTPM
Spleen	0.9 nTPM
Kidney	0.7 nTPM
Adipose tissue	0.5 nTPM
Stomach	0.4 nTPM
Breast	0.4 nTPM
Skeletal muscle	0.3 nTPM
Endometrium	0.2 nTPM
PBMC	0.1 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Basal keratinocytes	2.8 nTPM
Skin	2.8 nTPM

Basal squamous epithelial cells	11.4 nTPM
Esophagus	11.4 nTPM

Cholangiocytes	28.6 nTPM
Liver	28.6 nTPM

Distal enterocytes	30.4 nTPM
Rectum	51.5 nTPM
Colon	9.3 nTPM

Undifferentiated cells	39.6 nTPM
Rectum	62.2 nTPM
Small intestine	34.4 nTPM
Colon	22.1 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