Single cell type - CDCA4 - 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.	CDCA4
Gene descriptionⁱ Full gene name according to HGNC.	Cell division cycle associated 4
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.	2

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	Extravillous trophoblasts - 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 (Extravillous trophoblasts, Cytotrophoblasts, Spermatogonia, Suprabasal keratinocytes, Basal keratinocytes)
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 (Extravillous trophoblasts, Cytotrophoblasts, Spermatogonia, Suprabasal keratinocytes, Basal keratinocytes)

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

CDCA4 is part of cluster 38 Extravillous trophoblasts - Unknown function with confidenceⁱ 1
176 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
CKS1B	CDC28 protein kinase regulatory subunit 1B	0.8170	12
DYNC2I2	Dynein 2 intermediate chain 2	0.7112	38
RFC2	Replication factor C subunit 2	0.7039	12
POLR1G	RNA polymerase I subunit G	0.6917	38
HROB	Homologous recombination factor with OB-fold	0.6876	38
CENPQ	Centromere protein Q	0.6831	12
RAD51	RAD51 recombinase	0.6802	12
ERVMER34-1	Endogenous retrovirus group MER34 member 1, envelope	0.6726	38
RNASEH2A	Ribonuclease H2 subunit A	0.6693	12
H4C3	H4 clustered histone 3	0.6562	24
HAUS1	HAUS augmin like complex subunit 1	0.6555	12
CCNB1	Cyclin B1	0.6436	38
SKP2	S-phase kinase associated protein 2	0.6417	38
CDT1	Chromatin licensing and DNA replication factor 1	0.6411	12
MELK	Maternal embryonic leucine zipper kinase	0.6394	12

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	5.4 nTPM
Breast	7.6 nTPM
Adipose tissue	3.2 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	2.2 nTPM
Lung	2.2 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	7.4 nTPM
Liver	18.0 nTPM
Colon	17.6 nTPM
Spleen	5.8 nTPM
PBMC	5.7 nTPM
Breast	5.3 nTPM
Adipose tissue	5.0 nTPM
Bone marrow	4.9 nTPM
Kidney	4.8 nTPM
Stomach	4.5 nTPM
Lymph node	2.6 nTPM

Dendritic cells	11.5 nTPM
Breast	17.8 nTPM
Adipose tissue	12.8 nTPM
PBMC	4.0 nTPM

Endothelial cells	10.9 nTPM
Placenta	22.7 nTPM
Pancreas	19.3 nTPM
Skin	17.5 nTPM
Ovary	15.5 nTPM
Testis	11.2 nTPM
Endometrium	10.5 nTPM
Lung	9.3 nTPM
Prostate	8.7 nTPM
Liver	8.2 nTPM
Breast	8.2 nTPM
Skeletal muscle	8.0 nTPM
Heart muscle	5.0 nTPM
Eye	4.8 nTPM
Esophagus	3.6 nTPM

Fibroblasts	10.2 nTPM
Placenta	33.0 nTPM
Ovary	28.8 nTPM
Skin	13.8 nTPM
Breast	8.8 nTPM
Adipose tissue	6.3 nTPM
Esophagus	6.1 nTPM
Skeletal muscle	6.0 nTPM
Prostate	3.6 nTPM
Stomach	3.0 nTPM
Heart muscle	1.4 nTPM
Lung	1.2 nTPM

Intestinal goblet cells	6.6 nTPM
Small intestine	9.5 nTPM
Rectum	5.3 nTPM
Colon	5.0 nTPM

Macrophages	8.4 nTPM
Adipose tissue	17.0 nTPM
Prostate	16.0 nTPM
Pancreas	12.8 nTPM
Kidney	10.6 nTPM
Endometrium	10.6 nTPM
Spleen	10.4 nTPM
Stomach	8.8 nTPM
Breast	8.5 nTPM
Esophagus	7.9 nTPM
Skeletal muscle	6.4 nTPM
Ovary	6.4 nTPM
Testis	4.6 nTPM
Bone marrow	3.7 nTPM
Lung	2.4 nTPM
PBMC	0.0 nTPM

Paneth cells	3.3 nTPM
Rectum	6.1 nTPM
Small intestine	3.7 nTPM
Colon	0.0 nTPM

Plasma cells	11.8 nTPM
Bone marrow	33.0 nTPM
Spleen	14.9 nTPM
Stomach	5.8 nTPM
Adipose tissue	5.2 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	7.7 nTPM
Lung	8.7 nTPM
Bronchus	6.7 nTPM

Smooth muscle cells	12.5 nTPM
Pancreas	41.2 nTPM
Ovary	18.8 nTPM
Skin	13.6 nTPM
Endometrium	11.3 nTPM
Esophagus	10.9 nTPM
Heart muscle	10.8 nTPM
Prostate	8.2 nTPM
Skeletal muscle	6.4 nTPM
Breast	5.9 nTPM
Adipose tissue	5.2 nTPM
Bronchus	4.8 nTPM

T-cells	17.7 nTPM
Skin	45.1 nTPM
Kidney	30.2 nTPM
Colon	27.1 nTPM
Adipose tissue	23.0 nTPM
Bone marrow	20.0 nTPM
Prostate	19.0 nTPM
Ovary	17.8 nTPM
Liver	17.3 nTPM
PBMC	16.9 nTPM
Spleen	16.3 nTPM
Breast	16.3 nTPM
Skeletal muscle	14.2 nTPM
Stomach	10.7 nTPM
Endometrium	9.3 nTPM
Esophagus	6.6 nTPM
Lung	6.1 nTPM
Lymph node	4.9 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Cytotrophoblasts	84.5 nTPM
Placenta	84.5 nTPM

Distal enterocytes	4.3 nTPM
Colon	5.6 nTPM
Rectum	2.9 nTPM

Distal tubular cells	3.9 nTPM
Kidney	3.9 nTPM

Undifferentiated cells	9.5 nTPM
Small intestine	13.6 nTPM
Rectum	8.3 nTPM
Colon	6.7 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