Cell type atlas - COPE - The Human Protein Atlas

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COPE

SUMMARY

TISSUE

CELL TYPE

PATHOLOGY

BRAIN

BLOOD

CELL

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.	COPE
Gene descriptionⁱ Full gene name according to HGNC.	Coatomer protein complex subunit epsilon
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.	4

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
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
Blood 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 cell type specificity
Blood 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.	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.	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 (NX) 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 TISSUESⁱ Single cell RNA in cell types from tissue are shown separately for each analyzed tissue. For easier navigation across tissues, use the grey browser on the left side of the window. Barchart shows pTPM levels in each 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 Colon
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ RNA expression data (NX) of tissue culture cell lines.The analyzed cell lines are divided into 16 color-coded groups according to the organ they were obtained from. Detailed information about a specific cell line is revealed by hovering over the corresponding bar in the chart. The chart is clickable and redirects to more Cell Atlas data. Read more
Organ Expression Alphabetical

Alveolar cells type 1	3 NX
Lung	3 NX

Alveolar cells type 2	18 NX
Lung	18 NX

B-cells	183 NX
Liver	329 NX
Kidney	187 NX
Colon	179 NX

Basal glandular cells	156 NX
Prostate	156 NX

Basal keratinocytes	142 NX
Skin	142 NX

Bipolar cells	47 NX
Eye	47 NX

Cardiomyocytes	8 NX
Heart muscle	8 NX

Cholangiocytes	104 NX
Liver	104 NX

Ciliated cells	19 NX
Lung	19 NX

Club cells	14 NX
Lung	14 NX

Collecting duct cells	110 NX
Kidney	110 NX

Cone photoreceptor cells	28 NX
Eye	28 NX

Cytotrophoblasts	330 NX
Placenta	330 NX

Distal tubular cells	393 NX
Kidney	393 NX

Ductal cells	279 NX
Pancreas	279 NX

Early spermatids	142 NX
Testis	142 NX

Endothelial cells	116 NX
Placenta	240 NX
Pancreas	218 NX
Prostate	161 NX
Skin	148 NX
Testis	116 NX
Eye	112 NX
Liver	101 NX
Lung	18 NX
Heart muscle	7 NX

Enterocytes	396 NX
Colon	448 NX
Small intestine	331 NX
Rectum	187 NX

Erythroid cells	47 NX
Liver	47 NX

Exocrine glandular cells	322 NX
Pancreas	322 NX

Extravillous trophoblasts	363 NX
Placenta	363 NX

Fibroblasts	176 NX
Placenta	297 NX
Prostate	176 NX
Skin	168 NX
Lung	23 NX
Heart muscle	7 NX

Glandular cells	234 NX
Prostate	234 NX

Granulocytes	104 NX
Colon	165 NX
Lung	42 NX

Hepatocytes	138 NX
Liver	138 NX

Hofbauer cells	396 NX
Placenta	395 NX

Horizontal cells	54 NX
Eye	54 NX

Intestinal endocrine cells	162 NX
Colon	197 NX
Rectum	126 NX

Ito cells	109 NX
Liver	109 NX

Kupffer cells	192 NX
Liver	192 NX

Late spermatids	269 NX
Testis	269 NX

Leydig cells	134 NX
Testis	134 NX

Macrophages	268 NX
Pancreas	447 NX
Kidney	322 NX
Prostate	284 NX
Skin	280 NX
Testis	243 NX
Lung	31 NX

Melanocytes	233 NX
Skin	233 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	473 NX
Pancreas	473 NX

Mucus-secreting cells	210 NX
Colon	725 NX
Small intestine	266 NX
Rectum	178 NX

Muller glia cells	212 NX
Eye	212 NX

Pancreatic endocrine cells	289 NX
Pancreas	288 NX

Paneth cells	260 NX
Colon	680 NX
Small intestine	260 NX
Rectum	189 NX

Peritubular cells	125 NX
Testis	125 NX

Proximal tubular cells	313 NX
Kidney	313 NX

Rod photoreceptor cells	51 NX
Eye	51 NX

Sertoli cells	123 NX
Testis	123 NX

Smooth muscle cells	136 NX
Pancreas	374 NX
Prostate	138 NX
Skin	133 NX
Heart muscle	6 NX

Spermatocytes	176 NX
Testis	176 NX

Spermatogonia	228 NX
Testis	228 NX

Suprabasal keratinocytes	172 NX
Skin	172 NX

Syncytiotrophoblasts	453 NX
Placenta	453 NX

T-cells	205 NX
Kidney	265 NX
Skin	256 NX
Prostate	209 NX
Colon	205 NX
Liver	158 NX
Lung	50 NX

Undifferentiated cells	211 NX
Colon	419 NX
Small intestine	211 NX
Rectum	180 NX

Urothelial cells	224 NX
Prostate	224 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.