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.	Late 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.	Not detected
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.	Not detected
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 (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 RNA single cell type specificity: Not detected

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 11 Late spermatids - Unknown function with confidenceⁱ 1
430 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.
KCNK18	Potassium two pore domain channel subfamily K member 18	0.6870	11
LKAAEAR1	LKAAEAR motif containing 1	0.6771	11
KRTAP12-4	Keratin associated protein 12-4	0.6668	11
OR6P1	Olfactory receptor family 6 subfamily P member 1	0.6624	11
TNP1	Transition protein 1	0.6582	11
OR5K3	Olfactory receptor family 5 subfamily K member 3	0.6371	11
C10orf82	Chromosome 10 open reading frame 82	0.6342	11
GARIN5A	Golgi associated RAB2 interactor 5A	0.6341	11
IQCF2	IQ motif containing F2	0.6337	11
FAM229A	Family with sequence similarity 229 member A	0.6268	11
TRIM39-RPP21	TRIM39-RPP21 readthrough	0.6240	11
CCDC179	Coiled-coil domain containing 179	0.6212	11
OR11A1	Olfactory receptor family 11 subfamily A member 1	0.6199	11
C8orf74	Chromosome 8 open reading frame 74	0.6160	11
HMGB4	High mobility group box 4	0.6147	11

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