Single cell type - CYSTM1 - 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.	CYSTM1
Gene descriptionⁱ Full gene name according to HGNC.	Cysteine rich transmembrane module containing 1
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.	2

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	Pancreatic endocrine cells - Mixed function (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 (Distal tubular cells, Gastric mucus-secreting cells, Pancreatic endocrine cells, Late spermatids, Proximal tubular cells)
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 enriched (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 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. Read more	Cell line enhanced (OE19, RPTEC TERT1)
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 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 (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 (Distal tubular cells, Gastric mucus-secreting cells, Pancreatic endocrine cells, Late spermatids, Proximal tubular cells)

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

CYSTM1 is part of cluster 16 Pancreatic endocrine cells - Mixed function with confidenceⁱ 1
171 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
KPNA7	Karyopherin subunit alpha 7	0.7451	16
LAMA3	Laminin subunit alpha 3	0.7182	16
LAMC2	Laminin subunit gamma 2	0.7019	16
C19orf33	Chromosome 19 open reading frame 33	0.6955	16
SMIM31	Small integral membrane protein 31	0.6900	16
TFF1	Trefoil factor 1	0.6890	16
MMP1	Matrix metallopeptidase 1	0.6881	16
LYNX1-SLURP2	LYNX1-SLURP2 readthrough	0.6853	16
MUCL3	Mucin like 3	0.6801	16
CLTB	Clathrin light chain B	0.6766	16
MYEOV	Myeloma overexpressed	0.6764	16
FAM25G	Family with sequence similarity 25 member G	0.6731	16
LCE3E	Late cornified envelope 3E	0.6709	16
CBSL	Cystathionine beta-synthase like	0.6691	16
ANXA10	Annexin A10	0.6664	16

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	259.9 nTPM
Breast	294.7 nTPM
Adipose tissue	225.1 nTPM

Alveolar cells type 1	317.3 nTPM
Lung	317.3 nTPM

Alveolar cells type 2	115.2 nTPM
Lung	115.2 nTPM

Astrocytes	34.6 nTPM
Brain	34.6 nTPM

B-cells	52.8 nTPM
Colon	132.6 nTPM
Kidney	114.3 nTPM
Adipose tissue	101.8 nTPM
Stomach	56.8 nTPM
Breast	34.7 nTPM
Liver	31.7 nTPM
Bone marrow	16.4 nTPM
Spleen	15.3 nTPM
PBMC	12.9 nTPM
Lymph node	11.4 nTPM

Dendritic cells	42.8 nTPM
PBMC	71.8 nTPM
Adipose tissue	33.3 nTPM
Breast	23.3 nTPM

Distal enterocytes	1024.7 nTPM
Colon	1104.9 nTPM
Rectum	944.6 nTPM

Endothelial cells	147.8 nTPM
Prostate	436.5 nTPM
Skin	315.4 nTPM
Liver	244.0 nTPM
Breast	219.2 nTPM
Testis	143.4 nTPM
Heart muscle	102.4 nTPM
Skeletal muscle	102.2 nTPM
Pancreas	96.5 nTPM
Eye	93.1 nTPM
Placenta	90.4 nTPM
Esophagus	82.7 nTPM
Ovary	52.1 nTPM
Lung	46.8 nTPM
Endometrium	43.9 nTPM

Enteroendocrine cells	435.8 nTPM
Colon	476.1 nTPM
Rectum	395.6 nTPM

Fibroblasts	174.0 nTPM
Lung	557.4 nTPM
Prostate	388.0 nTPM
Adipose tissue	187.5 nTPM
Skin	163.0 nTPM
Heart muscle	144.1 nTPM
Breast	133.4 nTPM
Stomach	103.9 nTPM
Skeletal muscle	92.9 nTPM
Esophagus	79.3 nTPM
Placenta	46.3 nTPM
Ovary	18.7 nTPM

Intestinal goblet cells	285.8 nTPM
Colon	406.0 nTPM
Rectum	261.0 nTPM
Small intestine	190.6 nTPM

Macrophages	77.1 nTPM
Pancreas	237.4 nTPM
Kidney	198.1 nTPM
Prostate	119.3 nTPM
Adipose tissue	95.1 nTPM
Lung	77.3 nTPM
Ovary	69.8 nTPM
Endometrium	63.2 nTPM
Skeletal muscle	53.9 nTPM
Breast	50.1 nTPM
Stomach	43.9 nTPM
Bone marrow	40.0 nTPM
Testis	38.3 nTPM
Spleen	35.3 nTPM
Esophagus	34.6 nTPM
PBMC	0.0 nTPM

Paneth cells	1148.5 nTPM
Colon	1976.2 nTPM
Small intestine	822.2 nTPM
Rectum	647.1 nTPM

Plasma cells	37.4 nTPM
Stomach	75.8 nTPM
Adipose tissue	43.9 nTPM
Spleen	32.2 nTPM
Esophagus	18.4 nTPM
Bone marrow	16.5 nTPM

Respiratory ciliated cells	576.5 nTPM
Bronchus	688.0 nTPM
Lung	464.9 nTPM

Basal keratinocytes	169.5 nTPM
Skin	169.5 nTPM

Basal prostatic cells	525.6 nTPM
Prostate	525.6 nTPM

Basal respiratory cells	252.8 nTPM
Bronchus	252.8 nTPM

Basal squamous epithelial cells	51.2 nTPM
Esophagus	51.2 nTPM

Smooth muscle cells	190.6 nTPM
Prostate	352.3 nTPM
Heart muscle	249.9 nTPM
Breast	244.3 nTPM
Skin	221.8 nTPM
Adipose tissue	211.0 nTPM
Pancreas	198.1 nTPM
Esophagus	192.3 nTPM
Bronchus	144.6 nTPM
Skeletal muscle	130.5 nTPM
Ovary	82.5 nTPM
Endometrium	69.4 nTPM

T-cells	53.9 nTPM
Skin	177.3 nTPM
Prostate	137.3 nTPM
Kidney	100.7 nTPM
Colon	95.5 nTPM
Adipose tissue	85.7 nTPM
Lung	60.7 nTPM
Endometrium	55.8 nTPM
Stomach	39.0 nTPM
Skeletal muscle	36.6 nTPM
Breast	33.7 nTPM
Esophagus	26.2 nTPM
Liver	15.7 nTPM
Spleen	14.8 nTPM
Ovary	13.4 nTPM
Bone marrow	12.0 nTPM
PBMC	5.7 nTPM
Lymph node	5.7 nTPM

Undifferentiated cells	429.3 nTPM
Colon	563.6 nTPM
Rectum	452.1 nTPM
Small intestine	272.1 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