Single cell type - BCL3 - 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.	BCL3
Gene descriptionⁱ Full gene name according to HGNC.	BCL3 transcription coactivator
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Plasma proteins Transcription factors
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	Non-specific - Transcription (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 (Basal squamous epithelial cells, Squamous epithelial 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	Group enriched (neutrophil, eosinophil)
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, Karpas-707, SiHa)
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 (Basal squamous epithelial cells, Squamous epithelial 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

BCL3 is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
CDKN1A	Cyclin dependent kinase inhibitor 1A	0.6415	7
CSRNP1	Cysteine and serine rich nuclear protein 1	0.6091	7
NFKBIZ	NFKB inhibitor zeta	0.6010	41
DBNDD2	Dysbindin domain containing 2	0.5896	59
GNG10	G protein subunit gamma 10	0.5885	59
PNRC1	Proline rich nuclear receptor coactivator 1	0.5854	41
ERF	ETS2 repressor factor	0.5805	35
ADAT3	Adenosine deaminase tRNA specific 3	0.5683	61
RNASEK	Ribonuclease K	0.5674	59
PAM16	Presequence translocase associated motor 16	0.5654	59
NFKBIA	NFKB inhibitor alpha	0.5609	41
ZBTB2	Zinc finger and BTB domain containing 2	0.5602	44
CRTC2	CREB regulated transcription coactivator 2	0.5596	44
NOP2	NOP2 nucleolar protein	0.5550	59
ADM5	Adrenomedullin 5 (putative)	0.5549	14

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	56.3 nTPM
Adipose tissue	84.8 nTPM
Breast	27.7 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	51.3 nTPM
Lung	51.3 nTPM

Astrocytes	2.6 nTPM
Brain	2.6 nTPM

B-cells	43.9 nTPM
Lymph node	104.9 nTPM
Spleen	91.3 nTPM
Stomach	60.9 nTPM
Adipose tissue	47.1 nTPM
Bone marrow	40.9 nTPM
Breast	28.1 nTPM
Liver	25.9 nTPM
Kidney	23.8 nTPM
Colon	16.0 nTPM
PBMC	0.0 nTPM

Basal squamous epithelial cells	172.4 nTPM
Esophagus	172.4 nTPM

Dendritic cells	33.4 nTPM
Adipose tissue	51.4 nTPM
Breast	28.8 nTPM
PBMC	20.0 nTPM

Endothelial cells	76.3 nTPM
Esophagus	338.0 nTPM
Skeletal muscle	106.0 nTPM
Skin	102.2 nTPM
Endometrium	100.2 nTPM
Lung	81.1 nTPM
Liver	72.4 nTPM
Breast	66.5 nTPM
Prostate	63.1 nTPM
Testis	42.4 nTPM
Eye	29.9 nTPM
Placenta	27.3 nTPM
Ovary	17.7 nTPM
Heart muscle	13.6 nTPM
Pancreas	7.7 nTPM

Fibroblasts	47.8 nTPM
Stomach	170.7 nTPM
Skin	101.1 nTPM
Esophagus	64.6 nTPM
Lung	50.3 nTPM
Prostate	38.2 nTPM
Skeletal muscle	37.9 nTPM
Breast	31.9 nTPM
Adipose tissue	15.7 nTPM
Placenta	9.9 nTPM
Heart muscle	3.8 nTPM
Ovary	1.6 nTPM

Intestinal goblet cells	56.2 nTPM
Colon	99.3 nTPM
Rectum	43.1 nTPM
Small intestine	26.1 nTPM

Macrophages	86.6 nTPM
Stomach	228.5 nTPM
Spleen	207.3 nTPM
Adipose tissue	200.0 nTPM
Esophagus	132.2 nTPM
Bone marrow	108.7 nTPM
Skeletal muscle	88.5 nTPM
Prostate	76.8 nTPM
Endometrium	70.0 nTPM
Pancreas	51.0 nTPM
Kidney	49.9 nTPM
Breast	31.8 nTPM
Lung	28.7 nTPM
Ovary	15.4 nTPM
Testis	9.8 nTPM
PBMC	0.0 nTPM

Paneth cells	40.0 nTPM
Colon	56.0 nTPM
Small intestine	37.6 nTPM
Rectum	26.4 nTPM

Plasma cells	100.4 nTPM
Stomach	175.9 nTPM
Spleen	98.9 nTPM
Bone marrow	93.9 nTPM
Esophagus	92.4 nTPM
Adipose tissue	40.7 nTPM

Respiratory ciliated cells	20.5 nTPM
Bronchus	20.6 nTPM
Lung	20.4 nTPM

Smooth muscle cells	40.1 nTPM
Skin	96.9 nTPM
Esophagus	86.8 nTPM
Skeletal muscle	74.1 nTPM
Prostate	64.8 nTPM
Endometrium	32.4 nTPM
Adipose tissue	30.5 nTPM
Breast	20.0 nTPM
Pancreas	14.9 nTPM
Bronchus	11.4 nTPM
Ovary	6.2 nTPM
Heart muscle	3.3 nTPM

Cholangiocytes	42.9 nTPM
Liver	42.9 nTPM

Collecting duct cells	12.9 nTPM
Kidney	12.9 nTPM

Cytotrophoblasts	0.6 nTPM
Placenta	0.6 nTPM

Distal enterocytes	60.6 nTPM
Colon	71.8 nTPM
Rectum	49.3 nTPM

T-cells	46.2 nTPM
Spleen	184.3 nTPM
Lymph node	121.2 nTPM
Stomach	64.7 nTPM
Esophagus	58.9 nTPM
Adipose tissue	58.0 nTPM
Bone marrow	51.4 nTPM
Skin	44.2 nTPM
Endometrium	40.1 nTPM
Prostate	33.1 nTPM
Breast	29.1 nTPM
Skeletal muscle	28.3 nTPM
Lung	22.8 nTPM
Colon	21.4 nTPM
Kidney	15.8 nTPM
Liver	7.1 nTPM
PBMC	4.5 nTPM
Ovary	0.0 nTPM

Undifferentiated cells	34.5 nTPM
Colon	53.6 nTPM
Rectum	27.6 nTPM
Small intestine	22.4 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