Single cell type - COMMD3-BMI1 - 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.	COMMD3-BMI1
Gene descriptionⁱ Full gene name according to HGNC.	COMMD3-BMI1 readthrough
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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.	Plasma cells - Plasma cell differentiation (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.	Cell type enhanced (Epididymal clear cells, Parietal cells, Enterocytes, Thymic myoid cells, Epididymal efferent duct absorptive cells, Epididymal principal cells, Mast cells, Plasma cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.84
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Not available
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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

Single cell type

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Cell type enhanced (Reproductive supporting cells)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas HPA data, as well as data generated by Monaco et al and Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

COMMD3-BMI1 is part of cluster 67 Plasma cells - Plasma cell differentiation with confidenceⁱ 1
116 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
KRTCAP2	Keratinocyte associated protein 2	0.6698	67
IGLV1-40	Immunoglobulin lambda variable 1-40	0.6291	67
IGHV7-4-1	Immunoglobulin heavy variable 7-4-1	0.6223	67
IGLV7-43	Immunoglobulin lambda variable 7-43	0.6207	67
TXNDC5	Thioredoxin domain containing 5	0.6138	67
IGHV4-28	Immunoglobulin heavy variable 4-28	0.6114	67
IGHA1	Immunoglobulin heavy constant alpha 1	0.6090	67
IGHV3-13	Immunoglobulin heavy variable 3-13	0.6072	67
IGHV4-34	Immunoglobulin heavy variable 4-34	0.6072	67
BGLAP	Bone gamma-carboxyglutamate protein	0.6057	67
ENSG00000273047	Novel transcript, LIME1-SLC2A4RG readthrough	0.6015	67
IGHV1-24	Immunoglobulin heavy variable 1-24	0.6008	67
IGLL5	Immunoglobulin lambda like polypeptide 5	0.5979	67
JCHAIN	Joining chain of multimeric IgA and IgM	0.5974	67
RPL17	Ribosomal protein L17	0.5964	15

IMMUNE CELLS

COMMD3-BMI1 is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 0.99
519 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TOB1	Transducer of ERBB2, 1	1.0000	42
S1PR2	Sphingosine-1-phosphate receptor 2	1.0000	42
UGP2	UDP-glucose pyrophosphorylase 2	1.0000	42
ATXN7	Ataxin 7	1.0000	42
EIF2B2	Eukaryotic translation initiation factor 2B subunit beta	1.0000	42
CRBN	Cereblon	1.0000	42
CYLD	CYLD lysine 63 deubiquitinase	1.0000	42
POPDC2	Popeye domain containing 2	0.9762	42
RBSN	Rabenosyn, RAB effector	0.9762	42
PIM1	Pim-1 proto-oncogene, serine/threonine kinase	0.9762	42
MKRN2	Makorin ring finger protein 2	0.9762	42
C18orf21	Chromosome 18 open reading frame 21	0.9762	42
ADD3	Adducin 3	0.9762	42
ZNF394	Zinc finger protein 394	0.9762	42
CNOT2	CCR4-NOT transcription complex subunit 2	0.9762	42