Cell type atlas - LUM - The Human Protein Atlas

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LUM

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.	LUM
Gene descriptionⁱ Full gene name according to HGNC.	Lumican
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Plasma proteins
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	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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	Group enriched (Fibroblasts, Leydig 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 enriched (basophil)
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 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.	Cell line enriched (BJ hTERT+)
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 some
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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: Group enriched (Fibroblasts, Leydig 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	12 NX
Lung	12 NX

Alveolar cells type 2	51 NX
Lung	51 NX

B-cells	0 NX
Liver	1 NX
Kidney	0 NX
Colon	0 NX

Basal glandular cells	1 NX
Prostate	1 NX

Basal keratinocytes	87 NX
Skin	87 NX

Bipolar cells	0 NX
Eye	0 NX

Cardiomyocytes	10 NX
Heart muscle	10 NX

Cholangiocytes	0 NX
Liver	0 NX

Ciliated cells	1 NX
Lung	1 NX

Club cells	9 NX
Lung	9 NX

Collecting duct cells	0 NX
Kidney	0 NX

Cone photoreceptor cells	2 NX
Eye	2 NX

Cytotrophoblasts	47 NX
Placenta	47 NX

Distal tubular cells	0 NX
Kidney	0 NX

Ductal cells	1 NX
Pancreas	1 NX

Early spermatids	2 NX
Testis	2 NX

Endothelial cells	12 NX
Skin	92 NX
Lung	64 NX
Placenta	31 NX
Heart muscle	18 NX
Prostate	8 NX
Eye	2 NX
Testis	1 NX
Pancreas	0 NX
Liver	0 NX

Enterocytes	0 NX
Colon	0 NX
Rectum	0 NX
Small intestine	0 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	0 NX
Pancreas	0 NX

Extravillous trophoblasts	28 NX
Placenta	28 NX

Fibroblasts	1406 NX
Placenta	4037 NX
Skin	1761 NX
Prostate	1406 NX
Heart muscle	671 NX
Lung	452 NX

Glandular cells	2 NX
Prostate	2 NX

Granulocytes	17 NX
Lung	26 NX
Colon	9 NX

Hepatocytes	0 NX
Liver	0 NX

Hofbauer cells	59 NX
Placenta	59 NX

Horizontal cells	0 NX
Eye	0 NX

Intestinal endocrine cells	0 NX
Colon	0 NX
Rectum	0 NX

Ito cells	94 NX
Liver	94 NX

Kupffer cells	1 NX
Liver	1 NX

Late spermatids	3 NX
Testis	3 NX

Leydig cells	372 NX
Testis	372 NX

Macrophages	4 NX
Skin	106 NX
Lung	17 NX
Prostate	1 NX
Kidney	1 NX
Testis	1 NX
Pancreas	0 NX

Melanocytes	111 NX
Skin	111 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	2 NX
Pancreas	2 NX

Mucus-secreting cells	0 NX
Small intestine	1 NX
Colon	0 NX
Rectum	0 NX

Muller glia cells	76 NX
Eye	76 NX

Pancreatic endocrine cells	3 NX
Pancreas	3 NX

Paneth cells	0 NX
Rectum	0 NX
Colon	0 NX
Small intestine	0 NX

Peritubular cells	42 NX
Testis	42 NX

Proximal tubular cells	0 NX
Kidney	0 NX

Rod photoreceptor cells	3 NX
Eye	3 NX

Sertoli cells	0 NX
Testis	0 NX

Smooth muscle cells	68 NX
Pancreas	617 NX
Skin	134 NX
Prostate	68 NX
Heart muscle	20 NX

Spermatocytes	0 NX
Testis	0 NX

Spermatogonia	1 NX
Testis	1 NX

Suprabasal keratinocytes	88 NX
Skin	88 NX

Syncytiotrophoblasts	70 NX
Placenta	70 NX

T-cells	0 NX
Skin	91 NX
Lung	16 NX
Prostate	0 NX
Liver	0 NX
Kidney	0 NX
Colon	0 NX

Undifferentiated cells	0 NX
Rectum	0 NX
Small intestine	0 NX
Colon	0 NX

Urothelial cells	4 NX
Prostate	4 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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