Single cell type - MSL3 - 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.	MSL3
Gene descriptionⁱ Full gene name according to HGNC.	MSL complex subunit 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human disease 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	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	30

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	Low cell type specificity
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: Low cell type specificity

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

MSL3 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
JAML	Junction adhesion molecule like	0.6588	19
SELL	Selectin L	0.6449	63
EVI2B	Ecotropic viral integration site 2B	0.6007	19
MNDA	Myeloid cell nuclear differentiation antigen	0.5722	19
PARVG	Parvin gamma	0.5634	57
CCR2	C-C motif chemokine receptor 2	0.5606	19
CD1D	CD1d molecule	0.5513	57
EIF2S3	Eukaryotic translation initiation factor 2 subunit gamma	0.5385	32
CTSS	Cathepsin S	0.5320	19
CYBB	Cytochrome b-245 beta chain	0.5253	19
IL17RA	Interleukin 17 receptor A	0.5214	19
CLEC6A	C-type lectin domain containing 6A	0.5210	19
S100Z	S100 calcium binding protein Z	0.5200	19
CLEC4A	C-type lectin domain family 4 member A	0.5185	19
SP110	SP110 nuclear body protein	0.5184	57

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	30.1 nTPM
Breast	37.0 nTPM
Adipose tissue	23.2 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	19.2 nTPM
Lung	19.2 nTPM

Astrocytes	7.8 nTPM
Brain	7.8 nTPM

B-cells	52.7 nTPM
Adipose tissue	81.2 nTPM
Lymph node	74.6 nTPM
PBMC	65.7 nTPM
Spleen	56.8 nTPM
Bone marrow	49.8 nTPM
Colon	46.4 nTPM
Liver	46.3 nTPM
Stomach	43.6 nTPM
Breast	38.8 nTPM
Kidney	23.8 nTPM

Dendritic cells	73.5 nTPM
PBMC	111.6 nTPM
Adipose tissue	55.0 nTPM
Breast	53.9 nTPM

Endothelial cells	29.1 nTPM
Pancreas	54.0 nTPM
Heart muscle	52.4 nTPM
Ovary	37.2 nTPM
Endometrium	30.8 nTPM
Prostate	30.1 nTPM
Breast	29.1 nTPM
Esophagus	27.9 nTPM
Testis	25.2 nTPM
Lung	21.8 nTPM
Skeletal muscle	20.6 nTPM
Liver	20.2 nTPM
Skin	19.5 nTPM
Placenta	19.4 nTPM
Eye	18.6 nTPM

Fibroblasts	18.2 nTPM
Ovary	26.8 nTPM
Heart muscle	23.0 nTPM
Breast	21.5 nTPM
Lung	20.1 nTPM
Skeletal muscle	18.9 nTPM
Prostate	18.2 nTPM
Skin	18.2 nTPM
Adipose tissue	18.1 nTPM
Placenta	14.3 nTPM
Stomach	11.9 nTPM
Esophagus	8.7 nTPM

Intestinal goblet cells	16.4 nTPM
Colon	21.5 nTPM
Small intestine	15.4 nTPM
Rectum	12.3 nTPM

Macrophages	46.9 nTPM
Skeletal muscle	79.1 nTPM
Lung	78.2 nTPM
Adipose tissue	70.9 nTPM
Breast	61.7 nTPM
Spleen	57.0 nTPM
Esophagus	51.9 nTPM
Bone marrow	46.2 nTPM
Kidney	44.7 nTPM
Endometrium	42.7 nTPM
Testis	42.4 nTPM
Ovary	37.9 nTPM
Stomach	35.1 nTPM
Prostate	32.0 nTPM
Pancreas	23.0 nTPM
PBMC	0.0 nTPM

Paneth cells	8.7 nTPM
Colon	13.2 nTPM
Rectum	13.1 nTPM
Small intestine	0.0 nTPM

Plasma cells	41.3 nTPM
Adipose tissue	62.5 nTPM
Spleen	58.2 nTPM
Stomach	52.0 nTPM
Bone marrow	21.4 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	23.2 nTPM
Lung	29.1 nTPM
Bronchus	17.2 nTPM

Smooth muscle cells	21.8 nTPM
Ovary	35.6 nTPM
Pancreas	30.5 nTPM
Endometrium	29.5 nTPM
Breast	26.0 nTPM
Bronchus	18.9 nTPM
Esophagus	18.6 nTPM
Heart muscle	18.2 nTPM
Adipose tissue	17.9 nTPM
Skeletal muscle	17.6 nTPM
Prostate	15.3 nTPM
Skin	11.1 nTPM

T-cells	54.5 nTPM
Lymph node	151.5 nTPM
Lung	91.1 nTPM
Adipose tissue	88.1 nTPM
Spleen	80.9 nTPM
PBMC	75.2 nTPM
Breast	57.2 nTPM
Colon	46.6 nTPM
Esophagus	45.9 nTPM
Bone marrow	44.0 nTPM
Endometrium	41.0 nTPM
Kidney	40.4 nTPM
Skeletal muscle	40.3 nTPM
Stomach	32.1 nTPM
Liver	31.2 nTPM
Skin	25.7 nTPM
Prostate	19.0 nTPM
Ovary	15.6 nTPM

Basal keratinocytes	13.3 nTPM
Skin	13.3 nTPM

Basal prostatic cells	15.1 nTPM
Prostate	15.1 nTPM

Basal respiratory cells	10.7 nTPM
Bronchus	10.7 nTPM

Basal squamous epithelial cells	22.2 nTPM
Esophagus	22.2 nTPM

Undifferentiated cells	13.6 nTPM
Small intestine	16.4 nTPM
Rectum	13.3 nTPM
Colon	11.0 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