Single cell type - CNOT4 - 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.	CNOT4
Gene descriptionⁱ Full gene name according to HGNC.	CCR4-NOT transcription complex subunit 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins Transcription factors
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.	7

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 - 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

CNOT4 is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 1
482 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
MORC3	MORC family CW-type zinc finger 3	0.5367	10
ASH1L	ASH1 like histone lysine methyltransferase	0.5274	52
ILKAP	ILK associated serine/threonine phosphatase	0.5139	10
NIPBL	NIPBL cohesin loading factor	0.5130	10
CSNK1A1L	Casein kinase 1 alpha 1 like	0.5065	10
SF3A3	Splicing factor 3a subunit 3	0.4945	10
POTEF	POTE ankyrin domain family member F	0.4873	10
TBRG1	Transforming growth factor beta regulator 1	0.4818	10
DDX50	DExD-box helicase 50	0.4807	10
RABEP1	Rabaptin, RAB GTPase binding effector protein 1	0.4674	10
CDK12	Cyclin dependent kinase 12	0.4639	10
POTEE	POTE ankyrin domain family member E	0.4602	10
UBE3A	Ubiquitin protein ligase E3A	0.4488	10
SCFD1	Sec1 family domain containing 1	0.4473	55
C5orf34	Chromosome 5 open reading frame 34	0.4459	10

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	53.9 nTPM
Breast	64.0 nTPM
Adipose tissue	43.8 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	43.0 nTPM
Lung	43.0 nTPM

Astrocytes	83.9 nTPM
Brain	83.9 nTPM

B-cells	63.0 nTPM
Adipose tissue	80.2 nTPM
Colon	71.9 nTPM
Lymph node	71.5 nTPM
Bone marrow	68.7 nTPM
Spleen	67.5 nTPM
PBMC	62.8 nTPM
Kidney	61.9 nTPM
Stomach	58.5 nTPM
Breast	54.9 nTPM
Liver	31.6 nTPM

Dendritic cells	60.9 nTPM
Adipose tissue	88.5 nTPM
Breast	58.3 nTPM
PBMC	35.8 nTPM

Endothelial cells	48.3 nTPM
Prostate	93.5 nTPM
Skin	65.2 nTPM
Skeletal muscle	64.4 nTPM
Breast	57.7 nTPM
Heart muscle	55.8 nTPM
Esophagus	49.5 nTPM
Testis	47.1 nTPM
Endometrium	44.8 nTPM
Liver	38.5 nTPM
Ovary	36.9 nTPM
Placenta	35.3 nTPM
Lung	34.3 nTPM
Pancreas	30.9 nTPM
Eye	21.8 nTPM

Fibroblasts	58.4 nTPM
Prostate	91.4 nTPM
Skin	73.4 nTPM
Breast	72.5 nTPM
Skeletal muscle	64.4 nTPM
Esophagus	62.3 nTPM
Heart muscle	59.1 nTPM
Stomach	57.9 nTPM
Adipose tissue	51.0 nTPM
Placenta	40.5 nTPM
Lung	40.2 nTPM
Ovary	30.3 nTPM

Intestinal goblet cells	30.2 nTPM
Colon	38.6 nTPM
Rectum	27.5 nTPM
Small intestine	24.7 nTPM

Macrophages	33.4 nTPM
Breast	49.5 nTPM
Adipose tissue	47.2 nTPM
Ovary	42.8 nTPM
Spleen	41.4 nTPM
Skeletal muscle	39.8 nTPM
Lung	37.9 nTPM
Testis	37.8 nTPM
Prostate	34.4 nTPM
Kidney	34.0 nTPM
Endometrium	31.8 nTPM
Bone marrow	28.7 nTPM
Esophagus	26.8 nTPM
Pancreas	17.8 nTPM
Stomach	17.6 nTPM
PBMC	13.6 nTPM

Paneth cells	31.2 nTPM
Small intestine	37.6 nTPM
Colon	29.6 nTPM
Rectum	26.4 nTPM

Plasma cells	58.9 nTPM
Esophagus	80.1 nTPM
Adipose tissue	69.7 nTPM
Stomach	55.0 nTPM
Bone marrow	47.7 nTPM
Spleen	41.9 nTPM

Respiratory ciliated cells	35.4 nTPM
Bronchus	38.8 nTPM
Lung	32.1 nTPM

Smooth muscle cells	75.3 nTPM
Bronchus	244.9 nTPM
Skeletal muscle	75.1 nTPM
Esophagus	74.4 nTPM
Prostate	71.5 nTPM
Skin	67.0 nTPM
Heart muscle	63.7 nTPM
Breast	63.2 nTPM
Endometrium	51.2 nTPM
Ovary	48.2 nTPM
Adipose tissue	48.0 nTPM
Pancreas	20.9 nTPM

T-cells	61.6 nTPM
Prostate	108.9 nTPM
Colon	89.3 nTPM
Skeletal muscle	78.7 nTPM
Adipose tissue	74.2 nTPM
Breast	70.5 nTPM
PBMC	67.2 nTPM
Spleen	60.5 nTPM
Kidney	60.2 nTPM
Stomach	60.1 nTPM
Endometrium	59.6 nTPM
Bone marrow	54.1 nTPM
Lymph node	48.1 nTPM
Skin	47.5 nTPM
Liver	47.3 nTPM
Lung	45.6 nTPM
Ovary	42.2 nTPM
Esophagus	32.8 nTPM

Basal keratinocytes	67.7 nTPM
Skin	67.7 nTPM

Basal prostatic cells	76.3 nTPM
Prostate	76.3 nTPM

Basal respiratory cells	54.0 nTPM
Bronchus	54.0 nTPM

Basal squamous epithelial cells	45.5 nTPM
Esophagus	45.5 nTPM

Undifferentiated cells	29.3 nTPM
Colon	33.3 nTPM
Small intestine	28.2 nTPM
Rectum	26.3 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