Cell type atlas - LGI4 - The Human Protein Atlas

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LGI4

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.	LGI4
Gene descriptionⁱ Full gene name according to HGNC.	Leucine rich repeat LGI family member 4
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,Secreted
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	Group enriched (Smooth muscle cells, Muller glia cells, Sertoli 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 (plasmacytoid DC)
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 (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.	Detected in single
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 (Smooth muscle cells, Muller glia cells, Sertoli 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	0 NX
Lung	0 NX

Alveolar cells type 2	0 NX
Lung	0 NX

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

Basal glandular cells	0 NX
Prostate	0 NX

Basal keratinocytes	2 NX
Skin	2 NX

Bipolar cells	1 NX
Eye	1 NX

Cardiomyocytes	10 NX
Heart muscle	10 NX

Cholangiocytes	0 NX
Liver	0 NX

Ciliated cells	1 NX
Lung	1 NX

Club cells	1 NX
Lung	1 NX

Collecting duct cells	2 NX
Kidney	2 NX

Cone photoreceptor cells	2 NX
Eye	2 NX

Cytotrophoblasts	0 NX
Placenta	0 NX

Distal tubular cells	0 NX
Kidney	0 NX

Ductal cells	0 NX
Pancreas	0 NX

Early spermatids	0 NX
Testis	0 NX

Endothelial cells	2 NX
Heart muscle	13 NX
Skin	6 NX
Testis	5 NX
Prostate	3 NX
Eye	1 NX
Lung	0 NX
Pancreas	0 NX
Placenta	0 NX
Liver	0 NX

Enterocytes	2 NX
Rectum	15 NX
Colon	10 NX
Small intestine	0 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	0 NX
Pancreas	0 NX

Extravillous trophoblasts	0 NX
Placenta	0 NX

Fibroblasts	8 NX
Heart muscle	40 NX
Prostate	14 NX
Skin	11 NX
Lung	7 NX
Placenta	1 NX

Glandular cells	1 NX
Prostate	1 NX

Granulocytes	0 NX
Colon	0 NX
Lung	0 NX

Hepatocytes	2 NX
Liver	2 NX

Hofbauer cells	0 NX
Placenta	0 NX

Horizontal cells	0 NX
Eye	0 NX

Intestinal endocrine cells	2 NX
Colon	3 NX
Rectum	0 NX

Ito cells	13 NX
Liver	13 NX

Kupffer cells	0 NX
Liver	0 NX

Late spermatids	0 NX
Testis	0 NX

Leydig cells	14 NX
Testis	14 NX

Macrophages	1 NX
Skin	4 NX
Testis	2 NX
Prostate	1 NX
Lung	1 NX
Pancreas	0 NX
Kidney	0 NX

Melanocytes	10 NX
Skin	10 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	0 NX
Pancreas	0 NX

Mucus-secreting cells	0 NX
Colon	2 NX
Rectum	0 NX
Small intestine	0 NX

Muller glia cells	89 NX
Eye	89 NX

Pancreatic endocrine cells	0 NX
Pancreas	0 NX

Paneth cells	3 NX
Colon	55 NX
Rectum	3 NX
Small intestine	0 NX

Peritubular cells	7 NX
Testis	7 NX

Proximal tubular cells	0 NX
Kidney	0 NX

Rod photoreceptor cells	3 NX
Eye	3 NX

Sertoli cells	78 NX
Testis	78 NX

Smooth muscle cells	120 NX
Skin	180 NX
Prostate	143 NX
Heart muscle	120 NX
Pancreas	0 NX

Spermatocytes	1 NX
Testis	1 NX

Spermatogonia	1 NX
Testis	1 NX

Suprabasal keratinocytes	2 NX
Skin	2 NX

Syncytiotrophoblasts	0 NX
Placenta	0 NX

T-cells	0 NX
Skin	6 NX
Lung	2 NX
Kidney	1 NX
Colon	1 NX
Prostate	0 NX
Liver	0 NX

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

Urothelial cells	1 NX
Prostate	1 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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