Single cell type - CDK13 - 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.	CDK13
Gene descriptionⁱ Full gene name according to HGNC.	Cyclin dependent kinase 13
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Metabolic proteins Potential drug targets
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.	13

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 - Transcription (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 (Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor 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	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: Cell type enhanced (Oligodendrocytes, Excitatory neurons, Oligodendrocyte precursor 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

CDK13 is part of cluster 52 Non-specific - Transcription 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
KANSL1	KAT8 regulatory NSL complex subunit 1	0.6963	52
PAXBP1	PAX3 and PAX7 binding protein 1	0.5985	52
TRAPPC10	Trafficking protein particle complex 10	0.5818	63
ARID1B	AT-rich interaction domain 1B	0.5754	42
BRAF	B-Raf proto-oncogene, serine/threonine kinase	0.5740	52
DMTF1	Cyclin D binding myb like transcription factor 1	0.5626	52
LUC7L	LUC7 like	0.5582	52
ARGLU1	Arginine and glutamate rich 1	0.5570	52
PKN2	Protein kinase N2	0.5546	52
TUT4	Terminal uridylyl transferase 4	0.5528	7
CCNL2	Cyclin L2	0.5431	52
RBM26	RNA binding motif protein 26	0.5360	21
STRADA	STE20 related adaptor alpha	0.5349	42
INO80D	INO80 complex subunit D	0.5305	44
KANTR	KDM5C adjacent transcript	0.5226	7

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	47.6 nTPM
Adipose tissue	57.3 nTPM
Breast	37.9 nTPM

Alveolar cells type 1	44.8 nTPM
Lung	44.8 nTPM

Alveolar cells type 2	72.0 nTPM
Lung	72.0 nTPM

Astrocytes	131.6 nTPM
Brain	131.6 nTPM

B-cells	49.7 nTPM
Adipose tissue	119.3 nTPM
Breast	60.2 nTPM
PBMC	58.6 nTPM
Kidney	57.1 nTPM
Lymph node	52.2 nTPM
Bone marrow	36.8 nTPM
Stomach	34.9 nTPM
Colon	31.9 nTPM
Spleen	26.7 nTPM
Liver	19.3 nTPM

Dendritic cells	91.0 nTPM
Adipose tissue	150.2 nTPM
Breast	94.8 nTPM
PBMC	27.9 nTPM

Endothelial cells	30.9 nTPM
Heart muscle	57.3 nTPM
Endometrium	53.7 nTPM
Ovary	51.2 nTPM
Skeletal muscle	41.6 nTPM
Breast	35.6 nTPM
Lung	34.3 nTPM
Esophagus	28.3 nTPM
Testis	28.2 nTPM
Skin	25.8 nTPM
Prostate	25.0 nTPM
Eye	22.7 nTPM
Liver	11.9 nTPM
Placenta	9.1 nTPM
Pancreas	7.7 nTPM

Fibroblasts	31.7 nTPM
Heart muscle	49.1 nTPM
Adipose tissue	44.1 nTPM
Ovary	40.8 nTPM
Lung	39.1 nTPM
Breast	34.7 nTPM
Skeletal muscle	34.3 nTPM
Stomach	28.2 nTPM
Skin	23.0 nTPM
Prostate	22.0 nTPM
Esophagus	20.3 nTPM
Placenta	12.9 nTPM

Intestinal goblet cells	17.6 nTPM
Rectum	20.3 nTPM
Small intestine	19.1 nTPM
Colon	13.6 nTPM

Macrophages	31.6 nTPM
Adipose tissue	57.5 nTPM
Endometrium	52.3 nTPM
Ovary	45.3 nTPM
Breast	45.3 nTPM
Lung	38.6 nTPM
Esophagus	37.7 nTPM
Spleen	33.2 nTPM
Skeletal muscle	32.0 nTPM
Kidney	31.8 nTPM
Bone marrow	30.0 nTPM
Testis	22.6 nTPM
Stomach	17.6 nTPM
Pancreas	15.3 nTPM
Prostate	15.0 nTPM
PBMC	0.0 nTPM

Paneth cells	12.9 nTPM
Rectum	17.4 nTPM
Small intestine	11.3 nTPM
Colon	9.9 nTPM

Plasma cells	50.1 nTPM
Adipose tissue	167.0 nTPM
Esophagus	30.7 nTPM
Stomach	21.9 nTPM
Bone marrow	18.2 nTPM
Spleen	12.6 nTPM

Respiratory ciliated cells	32.8 nTPM
Lung	37.9 nTPM
Bronchus	27.7 nTPM

Smooth muscle cells	32.0 nTPM
Ovary	58.7 nTPM
Endometrium	53.7 nTPM
Adipose tissue	51.4 nTPM
Breast	34.8 nTPM
Heart muscle	34.0 nTPM
Skeletal muscle	26.5 nTPM
Bronchus	22.7 nTPM
Esophagus	18.6 nTPM
Prostate	17.5 nTPM
Skin	17.5 nTPM
Pancreas	16.6 nTPM

T-cells	49.7 nTPM
Adipose tissue	115.2 nTPM
Endometrium	106.1 nTPM
Breast	83.0 nTPM
Ovary	73.4 nTPM
Skeletal muscle	67.7 nTPM
Lymph node	46.6 nTPM
PBMC	43.3 nTPM
Kidney	43.1 nTPM
Esophagus	39.3 nTPM
Lung	38.0 nTPM
Bone marrow	32.8 nTPM
Liver	31.2 nTPM
Spleen	31.2 nTPM
Stomach	28.1 nTPM
Skin	24.9 nTPM
Colon	22.8 nTPM
Prostate	19.0 nTPM

Basal keratinocytes	21.4 nTPM
Skin	21.4 nTPM

Basal prostatic cells	18.5 nTPM
Prostate	18.5 nTPM

Basal respiratory cells	15.9 nTPM
Bronchus	15.9 nTPM

Basal squamous epithelial cells	29.0 nTPM
Esophagus	29.0 nTPM

Undifferentiated cells	20.1 nTPM
Rectum	22.7 nTPM
Colon	21.0 nTPM
Small intestine	16.6 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