Single cell type - CCND1 - 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.	CCND1
Gene descriptionⁱ Full gene name according to HGNC.	Cyclin D1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes FDA approved drug targets Human disease related genes
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	Pancreatic cells - Digestion (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 (Pancreatic endocrine cells, Ductal cells, Basal respiratory cells, Urothelial 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 (myeloid DC)
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 single
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 (U-266/70, WM-115)
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

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 (Pancreatic endocrine cells, Ductal cells, Basal respiratory cells, Urothelial 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

CCND1 is part of cluster 1 Pancreatic cells - Digestion with confidenceⁱ 1
148 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
AGRN	Agrin	0.7284	26
AJUBA	Ajuba LIM protein	0.6698	1
KRT81	Keratin 81	0.6633	1
KRT75	Keratin 75	0.6566	1
KRTAP2-3	Keratin associated protein 2-3	0.6525	1
ITGA3	Integrin subunit alpha 3	0.6435	1
IGFL1	IGF like family member 1	0.6341	26
SPOCD1	SPOC domain containing 1	0.6284	22
TGFA	Transforming growth factor alpha	0.6232	22
LCE3D	Late cornified envelope 3D	0.6196	16
CRCT1	Cysteine rich C-terminal 1	0.6134	16
AC008687.4	Novel protein	0.6047	16
CCDC9B	Coiled-coil domain containing 9B	0.6021	1
TRIM16	Tripartite motif containing 16	0.6014	61
LAMB3	Laminin subunit beta 3	0.5920	16

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	84.6 nTPM
Breast	134.2 nTPM
Adipose tissue	35.0 nTPM

Alveolar cells type 1	182.7 nTPM
Lung	182.7 nTPM

Alveolar cells type 2	115.6 nTPM
Lung	115.6 nTPM

Astrocytes	0.3 nTPM
Brain	0.3 nTPM

B-cells	8.3 nTPM
Colon	17.6 nTPM
Stomach	12.3 nTPM
Lymph node	10.8 nTPM
Spleen	10.4 nTPM
Kidney	9.5 nTPM
Breast	9.4 nTPM
PBMC	4.3 nTPM
Adipose tissue	4.0 nTPM
Bone marrow	2.5 nTPM
Liver	2.1 nTPM

Basal squamous epithelial cells	133.1 nTPM
Esophagus	133.1 nTPM

Dendritic cells	2.4 nTPM
Breast	6.5 nTPM
Adipose tissue	0.7 nTPM
PBMC	0.0 nTPM

Endothelial cells	141.0 nTPM
Ovary	457.2 nTPM
Pancreas	324.3 nTPM
Placenta	245.0 nTPM
Skin	186.2 nTPM
Lung	184.0 nTPM
Eye	144.8 nTPM
Breast	127.7 nTPM
Heart muscle	85.7 nTPM
Endometrium	64.2 nTPM
Prostate	49.6 nTPM
Skeletal muscle	49.2 nTPM
Esophagus	44.9 nTPM
Testis	10.1 nTPM
Liver	0.9 nTPM

Fibroblasts	67.6 nTPM
Prostate	290.4 nTPM
Skin	102.6 nTPM
Lung	81.5 nTPM
Breast	66.3 nTPM
Placenta	60.6 nTPM
Esophagus	37.7 nTPM
Heart muscle	34.9 nTPM
Stomach	25.3 nTPM
Skeletal muscle	20.9 nTPM
Adipose tissue	20.0 nTPM
Ovary	3.7 nTPM

Intestinal goblet cells	42.6 nTPM
Rectum	49.1 nTPM
Colon	48.6 nTPM
Small intestine	30.2 nTPM

Macrophages	23.6 nTPM
Breast	86.1 nTPM
Endometrium	61.8 nTPM
Esophagus	51.9 nTPM
Prostate	38.9 nTPM
Testis	19.7 nTPM
Kidney	19.6 nTPM
Skeletal muscle	19.6 nTPM
Lung	13.6 nTPM
PBMC	13.6 nTPM
Pancreas	12.8 nTPM
Adipose tissue	8.7 nTPM
Spleen	3.1 nTPM
Stomach	2.9 nTPM
Ovary	0.9 nTPM
Bone marrow	0.0 nTPM

Paneth cells	118.0 nTPM
Rectum	246.4 nTPM
Colon	62.6 nTPM
Small intestine	45.0 nTPM

Plasma cells	0.5 nTPM
Stomach	2.5 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	85.9 nTPM
Lung	86.0 nTPM
Bronchus	85.9 nTPM

Smooth muscle cells	184.8 nTPM
Pancreas	329.2 nTPM
Prostate	251.7 nTPM
Bronchus	238.2 nTPM
Skin	215.5 nTPM
Ovary	184.2 nTPM
Esophagus	172.1 nTPM
Endometrium	168.1 nTPM
Heart muscle	153.3 nTPM
Breast	145.0 nTPM
Adipose tissue	114.5 nTPM
Skeletal muscle	60.7 nTPM

Cholangiocytes	92.9 nTPM
Liver	92.9 nTPM

Collecting duct cells	125.0 nTPM
Kidney	125.0 nTPM

Cytotrophoblasts	10.9 nTPM
Placenta	10.9 nTPM

Distal enterocytes	44.8 nTPM
Colon	54.4 nTPM
Rectum	35.2 nTPM

T-cells	8.8 nTPM
Endometrium	29.2 nTPM
Skin	27.6 nTPM
Lung	18.2 nTPM
Breast	17.9 nTPM
Kidney	7.5 nTPM
Colon	7.1 nTPM
Esophagus	6.6 nTPM
Liver	6.0 nTPM
Lymph node	5.7 nTPM
Prostate	4.7 nTPM
Skeletal muscle	4.7 nTPM
Stomach	4.7 nTPM
Spleen	2.9 nTPM
Bone marrow	2.4 nTPM
Ovary	2.2 nTPM
Adipose tissue	1.6 nTPM
PBMC	1.2 nTPM

Undifferentiated cells	82.2 nTPM
Colon	115.7 nTPM
Small intestine	67.0 nTPM
Rectum	63.8 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