Cell type atlas - PICALM - The Human Protein Atlas

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PICALM

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.	PICALM
Gene descriptionⁱ Full gene name according to HGNC.	Phosphatidylinositol binding clathrin assembly protein
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes 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.	15

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	Cell type enhanced (neutrophil)
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	33 NX
Lung	33 NX

Alveolar cells type 2	64 NX
Lung	64 NX

B-cells	25 NX
Kidney	62 NX
Liver	25 NX
Colon	21 NX

Basal glandular cells	35 NX
Prostate	35 NX

Basal keratinocytes	103 NX
Skin	103 NX

Bipolar cells	20 NX
Eye	20 NX

Cardiomyocytes	40 NX
Heart muscle	40 NX

Cholangiocytes	33 NX
Liver	33 NX

Ciliated cells	32 NX
Lung	32 NX

Club cells	25 NX
Lung	25 NX

Collecting duct cells	68 NX
Kidney	68 NX

Cone photoreceptor cells	12 NX
Eye	12 NX

Cytotrophoblasts	37 NX
Placenta	37 NX

Distal tubular cells	27 NX
Kidney	27 NX

Ductal cells	54 NX
Pancreas	54 NX

Early spermatids	51 NX
Testis	51 NX

Endothelial cells	74 NX
Skin	113 NX
Lung	111 NX
Prostate	105 NX
Eye	92 NX
Testis	76 NX
Heart muscle	73 NX
Liver	70 NX
Pancreas	68 NX
Placenta	49 NX

Enterocytes	55 NX
Rectum	68 NX
Small intestine	63 NX
Colon	33 NX

Erythroid cells	70 NX
Liver	70 NX

Exocrine glandular cells	33 NX
Pancreas	33 NX

Extravillous trophoblasts	99 NX
Placenta	99 NX

Fibroblasts	46 NX
Lung	59 NX
Skin	57 NX
Heart muscle	46 NX
Prostate	38 NX
Placenta	31 NX

Glandular cells	38 NX
Prostate	38 NX

Granulocytes	47 NX
Colon	55 NX
Lung	40 NX

Hepatocytes	50 NX
Liver	50 NX

Hofbauer cells	74 NX
Placenta	74 NX

Horizontal cells	38 NX
Eye	38 NX

Intestinal endocrine cells	24 NX
Colon	27 NX
Rectum	21 NX

Ito cells	74 NX
Liver	74 NX

Kupffer cells	122 NX
Liver	122 NX

Late spermatids	73 NX
Testis	73 NX

Leydig cells	33 NX
Testis	33 NX

Macrophages	105 NX
Testis	162 NX
Skin	159 NX
Lung	116 NX
Kidney	108 NX
Prostate	102 NX
Pancreas	101 NX

Melanocytes	57 NX
Skin	57 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	47 NX
Pancreas	47 NX

Mucus-secreting cells	31 NX
Small intestine	35 NX
Rectum	29 NX
Colon	17 NX

Muller glia cells	21 NX
Eye	21 NX

Pancreatic endocrine cells	65 NX
Pancreas	65 NX

Paneth cells	46 NX
Colon	63 NX
Small intestine	46 NX
Rectum	40 NX

Peritubular cells	41 NX
Testis	41 NX

Proximal tubular cells	65 NX
Kidney	65 NX

Rod photoreceptor cells	17 NX
Eye	16 NX

Sertoli cells	78 NX
Testis	78 NX

Smooth muscle cells	78 NX
Skin	117 NX
Heart muscle	78 NX
Prostate	77 NX
Pancreas	55 NX

Spermatocytes	17 NX
Testis	17 NX

Spermatogonia	12 NX
Testis	12 NX

Suprabasal keratinocytes	84 NX
Skin	84 NX

Syncytiotrophoblasts	35 NX
Placenta	35 NX

T-cells	41 NX
Skin	54 NX
Kidney	45 NX
Liver	41 NX
Prostate	35 NX
Lung	26 NX
Colon	24 NX

Undifferentiated cells	25 NX
Small intestine	32 NX
Rectum	25 NX
Colon	14 NX

Urothelial cells	77 NX
Prostate	77 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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