Single cell type - PMS1 - 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.	PMS1
Gene descriptionⁱ Full gene name according to HGNC.	PMS1 homolog 1, mismatch repair system component
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.	16

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	Spermatids - Unknown 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	Group enriched (Late spermatids, Early spermatids)
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	Low immune cell specificity
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	Low cell line specificity
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: Group enriched (Late spermatids, Early spermatids)

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

PMS1 is part of cluster 34 Spermatids - Unknown function with confidenceⁱ 0.99
366 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
NOXRED1	NADP dependent oxidoreductase domain containing 1	0.8137	34
TMEM249	Transmembrane protein 249	0.7993	34
TAS2R1	Taste 2 receptor member 1	0.7692	34
ARL13A	ADP ribosylation factor like GTPase 13A	0.7673	34
CUL1	Cullin 1	0.7530	25
C9orf153	Chromosome 9 open reading frame 153	0.7503	34
DDX20	DEAD-box helicase 20	0.7356	34
GALNTL5	Polypeptide N-acetylgalactosaminyltransferase like 5	0.7208	25
SPATA9	Spermatogenesis associated 9	0.7115	34
NGLY1	N-glycanase 1	0.6933	25
CCDC126	Coiled-coil domain containing 126	0.6880	34
ADAM29	ADAM metallopeptidase domain 29	0.6880	34
TMEM191C	Transmembrane protein 191C	0.6850	34
TCP11X2	T-complex 11 family, X-linked 2	0.6730	25
NBPF4	NBPF member 4	0.6628	34

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	18.5 nTPM
Breast	22.9 nTPM
Adipose tissue	14.2 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	14.4 nTPM
Lung	14.4 nTPM

Astrocytes	45.1 nTPM
Brain	45.1 nTPM

B-cells	22.7 nTPM
Lymph node	39.4 nTPM
Bone marrow	38.5 nTPM
Spleen	36.4 nTPM
Stomach	33.2 nTPM
Breast	17.3 nTPM
PBMC	17.1 nTPM
Adipose tissue	14.6 nTPM
Liver	12.7 nTPM
Kidney	9.5 nTPM
Colon	8.0 nTPM

Dendritic cells	18.7 nTPM
PBMC	23.9 nTPM
Breast	18.9 nTPM
Adipose tissue	13.3 nTPM

Endothelial cells	14.8 nTPM
Lung	24.9 nTPM
Esophagus	23.2 nTPM
Heart muscle	22.4 nTPM
Breast	19.1 nTPM
Placenta	18.2 nTPM
Endometrium	17.5 nTPM
Eye	13.7 nTPM
Testis	13.3 nTPM
Ovary	13.3 nTPM
Skeletal muscle	12.9 nTPM
Skin	9.5 nTPM
Prostate	8.2 nTPM
Liver	6.4 nTPM
Pancreas	3.9 nTPM

Fibroblasts	18.5 nTPM
Heart muscle	38.1 nTPM
Lung	29.0 nTPM
Breast	23.1 nTPM
Esophagus	18.3 nTPM
Skeletal muscle	18.0 nTPM
Ovary	17.9 nTPM
Stomach	16.3 nTPM
Adipose tissue	15.9 nTPM
Placenta	12.7 nTPM
Skin	7.3 nTPM
Prostate	6.7 nTPM

Intestinal goblet cells	7.3 nTPM
Small intestine	8.9 nTPM
Rectum	6.6 nTPM
Colon	6.5 nTPM

Macrophages	14.9 nTPM
Testis	33.7 nTPM
Ovary	27.2 nTPM
Bone marrow	17.5 nTPM
Breast	16.6 nTPM
Spleen	14.5 nTPM
PBMC	13.6 nTPM
Adipose tissue	13.6 nTPM
Endometrium	13.3 nTPM
Skeletal muscle	13.1 nTPM
Lung	12.5 nTPM
Stomach	11.7 nTPM
Prostate	10.3 nTPM
Kidney	9.9 nTPM
Esophagus	7.9 nTPM
Pancreas	7.7 nTPM

Paneth cells	4.3 nTPM
Small intestine	7.5 nTPM
Rectum	5.2 nTPM
Colon	0.0 nTPM

Plasma cells	30.1 nTPM
Spleen	41.0 nTPM
Stomach	38.5 nTPM
Bone marrow	34.6 nTPM
Esophagus	30.7 nTPM
Adipose tissue	5.8 nTPM

Respiratory ciliated cells	27.0 nTPM
Lung	42.3 nTPM
Bronchus	11.7 nTPM

Smooth muscle cells	15.0 nTPM
Heart muscle	40.3 nTPM
Breast	19.0 nTPM
Endometrium	18.3 nTPM
Esophagus	17.0 nTPM
Adipose tissue	13.9 nTPM
Ovary	13.6 nTPM
Pancreas	12.1 nTPM
Skeletal muscle	11.8 nTPM
Prostate	7.8 nTPM
Skin	6.0 nTPM
Bronchus	5.6 nTPM

T-cells	20.9 nTPM
Lung	41.0 nTPM
Bone marrow	36.3 nTPM
Spleen	29.9 nTPM
Stomach	28.7 nTPM
Kidney	25.3 nTPM
Breast	23.6 nTPM
Lymph node	23.2 nTPM
Ovary	20.1 nTPM
Esophagus	19.7 nTPM
Skeletal muscle	18.5 nTPM
Endometrium	15.8 nTPM
Liver	15.2 nTPM
PBMC	15.0 nTPM
Prostate	14.2 nTPM
Colon	10.5 nTPM
Adipose tissue	10.4 nTPM
Skin	8.3 nTPM

Basal keratinocytes	6.9 nTPM
Skin	6.9 nTPM

Basal squamous epithelial cells	21.6 nTPM
Esophagus	21.6 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Collecting duct cells	5.5 nTPM
Kidney	5.5 nTPM

Undifferentiated cells	11.1 nTPM
Small intestine	12.7 nTPM
Rectum	11.1 nTPM
Colon	9.4 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