Single cell type - BMS1 - 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.	BMS1
Gene descriptionⁱ Full gene name according to HGNC.	BMS1 ribosome biogenesis factor
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.	1

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	Non-specific - 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	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 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	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

BMS1 is part of cluster 10 Non-specific - Unknown function with confidenceⁱ 0.98
482 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
LTV1	LTV1 ribosome biogenesis factor	0.5266	39
MAK16	MAK16 homolog	0.5056	10
U2SURP	U2 snRNP associated SURP domain containing	0.4996	10
XRCC5	X-ray repair cross complementing 5	0.4992	10
GTPBP4	GTP binding protein 4	0.4964	44
CCT6A	Chaperonin containing TCP1 subunit 6A	0.4918	39
PRPF40A	Pre-mRNA processing factor 40 homolog A	0.4839	10
GNL2	G protein nucleolar 2	0.4794	10
THRAP3	Thyroid hormone receptor associated protein 3	0.4671	10
SLK	STE20 like kinase	0.4671	22
WDR3	WD repeat domain 3	0.4667	13
MPHOSPH10	M-phase phosphoprotein 10	0.4660	10
NOP14	NOP14 nucleolar protein	0.4653	10
HNRNPR	Heterogeneous nuclear ribonucleoprotein R	0.4648	10
TRMT6	TRNA methyltransferase 6	0.4638	10

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	25.6 nTPM
Adipose tissue	25.7 nTPM
Breast	25.5 nTPM

Alveolar cells type 1	32.1 nTPM
Lung	32.1 nTPM

Alveolar cells type 2	33.1 nTPM
Lung	33.1 nTPM

Astrocytes	19.6 nTPM
Brain	19.6 nTPM

B-cells	29.7 nTPM
Kidney	42.9 nTPM
Liver	36.8 nTPM
PBMC	34.3 nTPM
Stomach	34.1 nTPM
Adipose tissue	33.0 nTPM
Breast	26.8 nTPM
Spleen	26.0 nTPM
Bone marrow	23.7 nTPM
Colon	20.8 nTPM
Lymph node	18.9 nTPM

Dendritic cells	23.6 nTPM
Adipose tissue	38.7 nTPM
Breast	24.1 nTPM
PBMC	8.0 nTPM

Endothelial cells	31.3 nTPM
Pancreas	54.0 nTPM
Lung	46.8 nTPM
Ovary	37.8 nTPM
Endometrium	37.4 nTPM
Prostate	35.2 nTPM
Heart muscle	32.4 nTPM
Testis	28.8 nTPM
Skeletal muscle	28.5 nTPM
Eye	28.3 nTPM
Skin	24.0 nTPM
Placenta	23.9 nTPM
Esophagus	21.2 nTPM
Liver	21.1 nTPM
Breast	18.2 nTPM

Fibroblasts	26.4 nTPM
Heart muscle	48.0 nTPM
Lung	47.0 nTPM
Prostate	28.7 nTPM
Skeletal muscle	28.6 nTPM
Ovary	28.5 nTPM
Placenta	22.1 nTPM
Adipose tissue	21.4 nTPM
Skin	20.8 nTPM
Breast	19.1 nTPM
Stomach	13.4 nTPM
Esophagus	12.7 nTPM

Intestinal goblet cells	11.5 nTPM
Rectum	13.4 nTPM
Colon	12.1 nTPM
Small intestine	9.0 nTPM

Macrophages	19.9 nTPM
Lung	33.2 nTPM
Endometrium	31.1 nTPM
PBMC	27.3 nTPM
Kidney	23.4 nTPM
Pancreas	23.0 nTPM
Adipose tissue	22.2 nTPM
Breast	22.0 nTPM
Prostate	21.8 nTPM
Skeletal muscle	21.3 nTPM
Ovary	19.3 nTPM
Spleen	13.5 nTPM
Testis	12.8 nTPM
Stomach	11.7 nTPM
Bone marrow	10.0 nTPM
Esophagus	6.3 nTPM

Paneth cells	8.9 nTPM
Rectum	15.9 nTPM
Small intestine	7.5 nTPM
Colon	3.3 nTPM

Plasma cells	31.3 nTPM
Adipose tissue	39.4 nTPM
Bone marrow	37.9 nTPM
Stomach	34.0 nTPM
Spleen	27.0 nTPM
Esophagus	18.4 nTPM

Respiratory ciliated cells	49.5 nTPM
Lung	74.4 nTPM
Bronchus	24.7 nTPM

Smooth muscle cells	31.4 nTPM
Heart muscle	76.5 nTPM
Ovary	40.6 nTPM
Pancreas	38.4 nTPM
Bronchus	35.9 nTPM
Skeletal muscle	28.9 nTPM
Endometrium	28.1 nTPM
Breast	26.0 nTPM
Prostate	22.8 nTPM
Adipose tissue	21.1 nTPM
Skin	18.8 nTPM
Esophagus	7.8 nTPM

T-cells	25.3 nTPM
Lung	45.6 nTPM
Skin	36.4 nTPM
Adipose tissue	35.6 nTPM
Endometrium	32.5 nTPM
Skeletal muscle	31.1 nTPM
PBMC	28.9 nTPM
Breast	26.8 nTPM
Kidney	26.7 nTPM
Stomach	26.1 nTPM
Ovary	24.5 nTPM
Liver	20.5 nTPM
Spleen	20.5 nTPM
Lymph node	20.1 nTPM
Colon	20.0 nTPM
Bone marrow	19.2 nTPM
Prostate	9.5 nTPM
Esophagus	6.6 nTPM

Basal keratinocytes	22.9 nTPM
Skin	22.9 nTPM

Basal prostatic cells	33.9 nTPM
Prostate	33.9 nTPM

Basal respiratory cells	28.4 nTPM
Bronchus	28.4 nTPM

Basal squamous epithelial cells	14.2 nTPM
Esophagus	14.2 nTPM

Undifferentiated cells	18.7 nTPM
Colon	20.9 nTPM
Rectum	17.8 nTPM
Small intestine	17.3 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