Single cell type - LYST - The Human Protein Atlas

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 Human 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 expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Monocytes & Neutrophils - Innate immune response (mainly)
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)
Immune 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	Immune cell enhanced (neutrophil)
Immune 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. Read more	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. Read more	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 (nTPM) 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)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

LYST is part of cluster 19 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 1
175 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
ADGRE3	Adhesion G protein-coupled receptor E3	0.5747	19
AGO4	Argonaute RISC component 4	0.5735	19
C19orf38	Chromosome 19 open reading frame 38	0.5411	19
TMEM170B	Transmembrane protein 170B	0.5398	19
LILRA1	Leukocyte immunoglobulin like receptor A1	0.5335	19
NLRP12	NLR family pyrin domain containing 12	0.5234	19
ADGRE1	Adhesion G protein-coupled receptor E1	0.5225	19
MEFV	MEFV innate immuity regulator, pyrin	0.5222	19
SLC2A6	Solute carrier family 2 member 6	0.5218	19
CLEC12A	C-type lectin domain family 12 member A	0.5140	19
S100Z	S100 calcium binding protein Z	0.5136	19
PHF20L1	PHD finger protein 20 like 1	0.5129	51
FCN1	Ficolin 1	0.5123	19
S100A12	S100 calcium binding protein A12	0.5111	19
OSBPL8	Oxysterol binding protein like 8	0.5078	19

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated 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 Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	66.3 nTPM
Adipose tissue	100.6 nTPM
Breast	32.0 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	41.1 nTPM
Lung	41.1 nTPM

Astrocytes	71.2 nTPM
Brain	71.2 nTPM

B-cells	70.9 nTPM
Adipose tissue	144.4 nTPM
Colon	108.6 nTPM
PBMC	91.3 nTPM
Bone marrow	77.6 nTPM
Lymph node	69.9 nTPM
Spleen	58.2 nTPM
Stomach	53.6 nTPM
Kidney	42.9 nTPM
Breast	38.8 nTPM
Liver	23.7 nTPM

Dendritic cells	77.3 nTPM
Adipose tissue	154.1 nTPM
Breast	74.0 nTPM
PBMC	4.0 nTPM

Endothelial cells	51.2 nTPM
Testis	149.9 nTPM
Heart muscle	81.1 nTPM
Esophagus	80.2 nTPM
Breast	57.3 nTPM
Skeletal muscle	54.4 nTPM
Skin	51.0 nTPM
Lung	49.9 nTPM
Prostate	48.4 nTPM
Eye	41.2 nTPM
Liver	35.7 nTPM
Placenta	19.9 nTPM
Ovary	18.3 nTPM
Endometrium	18.0 nTPM
Pancreas	11.6 nTPM

Fibroblasts	27.0 nTPM
Prostate	50.2 nTPM
Heart muscle	35.3 nTPM
Skin	33.4 nTPM
Adipose tissue	32.7 nTPM
Skeletal muscle	30.8 nTPM
Esophagus	27.5 nTPM
Stomach	26.7 nTPM
Breast	21.7 nTPM
Lung	20.1 nTPM
Ovary	9.5 nTPM
Placenta	8.7 nTPM

Intestinal goblet cells	14.3 nTPM
Small intestine	14.7 nTPM
Rectum	14.6 nTPM
Colon	13.6 nTPM

Macrophages	111.4 nTPM
Spleen	232.3 nTPM
Bone marrow	211.2 nTPM
Stomach	190.5 nTPM
Kidney	175.4 nTPM
Skeletal muscle	142.0 nTPM
PBMC	122.7 nTPM
Lung	109.4 nTPM
Adipose tissue	105.0 nTPM
Prostate	80.2 nTPM
Esophagus	67.7 nTPM
Testis	65.0 nTPM
Endometrium	57.1 nTPM
Breast	47.8 nTPM
Pancreas	33.2 nTPM
Ovary	32.1 nTPM

Paneth cells	24.2 nTPM
Colon	49.4 nTPM
Rectum	15.7 nTPM
Small intestine	7.5 nTPM

Plasma cells	37.3 nTPM
Adipose tissue	130.9 nTPM
Esophagus	18.4 nTPM
Stomach	14.1 nTPM
Bone marrow	11.5 nTPM
Spleen	11.4 nTPM

Respiratory ciliated cells	26.7 nTPM
Bronchus	27.2 nTPM
Lung	26.2 nTPM

Smooth muscle cells	22.7 nTPM
Prostate	33.4 nTPM
Heart muscle	31.5 nTPM
Adipose tissue	30.1 nTPM
Esophagus	29.4 nTPM
Skin	28.6 nTPM
Skeletal muscle	21.4 nTPM
Endometrium	19.6 nTPM
Bronchus	18.0 nTPM
Breast	15.8 nTPM
Pancreas	11.2 nTPM
Ovary	10.4 nTPM

T-cells	71.3 nTPM
Adipose tissue	145.6 nTPM
Colon	121.7 nTPM
Spleen	105.7 nTPM
Lung	97.2 nTPM
Skeletal muscle	95.0 nTPM
Bone marrow	82.8 nTPM
Liver	73.8 nTPM
Prostate	71.1 nTPM
Esophagus	58.9 nTPM
Lymph node	57.0 nTPM
Skin	50.2 nTPM
Endometrium	49.2 nTPM
Stomach	48.1 nTPM
Kidney	43.1 nTPM
Breast	41.9 nTPM
Ovary	37.8 nTPM
PBMC	33.6 nTPM

Basal keratinocytes	71.0 nTPM
Skin	71.0 nTPM

Basal prostatic cells	89.8 nTPM
Prostate	89.8 nTPM

Basal squamous epithelial cells	18.8 nTPM
Esophagus	18.8 nTPM

Collecting duct cells	11.0 nTPM
Kidney	11.0 nTPM

Undifferentiated cells	7.6 nTPM
Rectum	9.0 nTPM
Colon	8.5 nTPM
Small intestine	5.3 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC