Cell type atlas - LYST - The Human Protein Atlas

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LYST

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.	LYST
Gene descriptionⁱ Full gene name according to HGNC.	Lysosomal trafficking regulator
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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.	3

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	Cell type enhanced (monocytes, Rod photoreceptor cells)
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 many
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.	Cell line enhanced (HDLM-2, SK-MEL-30, THP-1, U-937)
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 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 (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: Cell type enhanced (monocytes, Rod photoreceptor cells)

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	18 NX
Lung	18 NX

Alveolar cells type 2	50 NX
Lung	50 NX

B-cells	48 NX
Colon	102 NX
Kidney	40 NX
Liver	32 NX

Basal glandular cells	72 NX
Prostate	72 NX

Basal keratinocytes	63 NX
Skin	63 NX

Bipolar cells	62 NX
Eye	62 NX

Cardiomyocytes	9 NX
Heart muscle	9 NX

Cholangiocytes	10 NX
Liver	10 NX

Ciliated cells	24 NX
Lung	24 NX

Club cells	40 NX
Lung	40 NX

Collecting duct cells	10 NX
Kidney	10 NX

Cone photoreceptor cells	88 NX
Eye	88 NX

Cytotrophoblasts	5 NX
Placenta	5 NX

Distal tubular cells	10 NX
Kidney	10 NX

Ductal cells	6 NX
Pancreas	6 NX

Early spermatids	10 NX
Testis	10 NX

Endothelial cells	42 NX
Testis	138 NX
Heart muscle	87 NX
Lung	47 NX
Skin	45 NX
Prostate	42 NX
Eye	38 NX
Liver	34 NX
Placenta	19 NX
Pancreas	11 NX

Enterocytes	12 NX
Rectum	21 NX
Colon	16 NX
Small intestine	11 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	11 NX
Pancreas	11 NX

Extravillous trophoblasts	4 NX
Placenta	4 NX

Fibroblasts	24 NX
Prostate	44 NX
Heart muscle	33 NX
Skin	26 NX
Lung	19 NX
Placenta	8 NX

Glandular cells	49 NX
Prostate	49 NX

Granulocytes	107 NX
Lung	158 NX
Colon	55 NX

Hepatocytes	15 NX
Liver	15 NX

Hofbauer cells	28 NX
Placenta	28 NX

Horizontal cells	49 NX
Eye	49 NX

Intestinal endocrine cells	9 NX
Rectum	12 NX
Colon	7 NX

Ito cells	15 NX
Liver	15 NX

Kupffer cells	73 NX
Liver	73 NX

Late spermatids	13 NX
Testis	13 NX

Leydig cells	26 NX
Testis	26 NX

Macrophages	70 NX
Kidney	157 NX
Lung	112 NX
Prostate	74 NX
Skin	68 NX
Testis	60 NX
Pancreas	30 NX

Melanocytes	115 NX
Skin	115 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	236 NX
Pancreas	236 NX

Mucus-secreting cells	11 NX
Small intestine	16 NX
Colon	12 NX
Rectum	11 NX

Muller glia cells	24 NX
Eye	24 NX

Pancreatic endocrine cells	24 NX
Pancreas	24 NX

Paneth cells	14 NX
Colon	43 NX
Rectum	14 NX
Small intestine	7 NX

Peritubular cells	21 NX
Testis	21 NX

Proximal tubular cells	9 NX
Kidney	9 NX

Rod photoreceptor cells	167 NX
Eye	167 NX

Sertoli cells	13 NX
Testis	13 NX

Smooth muscle cells	29 NX
Prostate	30 NX
Heart muscle	29 NX
Skin	25 NX
Pancreas	10 NX

Spermatocytes	80 NX
Testis	80 NX

Spermatogonia	23 NX
Testis	23 NX

Suprabasal keratinocytes	57 NX
Skin	57 NX

Syncytiotrophoblasts	7 NX
Placenta	7 NX

T-cells	65 NX
Colon	112 NX
Lung	92 NX
Liver	70 NX
Prostate	65 NX
Skin	45 NX
Kidney	40 NX

Undifferentiated cells	6 NX
Rectum	7 NX
Colon	6 NX
Small intestine	4 NX

Urothelial cells	83 NX
Prostate	83 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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