Single cell type - COMMD5 - 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.	COMMD5
Gene descriptionⁱ Full gene name according to HGNC.	COMM domain containing 5
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.	6

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	Macrophages - 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

COMMD5 is part of cluster 41 Macrophages - Immune response with confidenceⁱ 1
307 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
SLAMF8	SLAM family member 8	0.5267	4
RNH1	Ribonuclease/angiogenin inhibitor 1	0.5239	4
RIT1	Ras like without CAAX 1	0.5231	41
CCL4L2	C-C motif chemokine ligand 4 like 2	0.5184	63
SMIM12	Small integral membrane protein 12	0.5144	39
ARL4C	ADP ribosylation factor like GTPase 4C	0.5060	24
NUBP1	Nucleotide binding protein 1	0.5046	3
NINJ1	Ninjurin 1	0.5029	41
RAB9A	RAB9A, member RAS oncogene family	0.5000	24
ATP6AP2	ATPase H+ transporting accessory protein 2	0.4993	4
CLPTM1	CLPTM1 regulator of GABA type A receptor forward trafficking	0.4979	55
PDCL3	Phosducin like 3	0.4945	24
BLOC1S2	Biogenesis of lysosomal organelles complex 1 subunit 2	0.4913	26
HAVCR2	Hepatitis A virus cellular receptor 2	0.4882	63
CTSZ	Cathepsin Z	0.4838	41

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	27.8 nTPM
Breast	35.9 nTPM
Adipose tissue	19.7 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	15.0 nTPM
Lung	15.0 nTPM

Astrocytes	8.5 nTPM
Brain	8.5 nTPM

B-cells	27.5 nTPM
Colon	52.7 nTPM
Stomach	37.7 nTPM
Adipose tissue	35.1 nTPM
Spleen	29.7 nTPM
Kidney	28.5 nTPM
Liver	25.5 nTPM
Breast	21.3 nTPM
Bone marrow	16.4 nTPM
PBMC	14.3 nTPM
Lymph node	13.7 nTPM

Dendritic cells	39.0 nTPM
Adipose tissue	57.3 nTPM
Breast	43.8 nTPM
PBMC	16.0 nTPM

Endothelial cells	27.6 nTPM
Pancreas	46.4 nTPM
Prostate	42.9 nTPM
Eye	36.4 nTPM
Heart muscle	34.3 nTPM
Placenta	32.9 nTPM
Ovary	32.0 nTPM
Testis	26.1 nTPM
Breast	26.1 nTPM
Skin	24.5 nTPM
Esophagus	22.1 nTPM
Skeletal muscle	20.0 nTPM
Endometrium	18.6 nTPM
Liver	18.3 nTPM
Lung	6.2 nTPM

Fibroblasts	22.7 nTPM
Prostate	33.3 nTPM
Breast	31.1 nTPM
Skin	26.8 nTPM
Heart muscle	26.5 nTPM
Placenta	25.4 nTPM
Adipose tissue	23.9 nTPM
Skeletal muscle	21.9 nTPM
Ovary	21.6 nTPM
Esophagus	21.6 nTPM
Stomach	11.9 nTPM
Lung	5.6 nTPM

Intestinal goblet cells	16.8 nTPM
Colon	20.1 nTPM
Small intestine	16.0 nTPM
Rectum	14.4 nTPM

Macrophages	34.2 nTPM
Ovary	67.9 nTPM
Pancreas	61.2 nTPM
Kidney	48.5 nTPM
Prostate	48.2 nTPM
Adipose tissue	43.7 nTPM
Breast	34.4 nTPM
Stomach	32.2 nTPM
Testis	29.7 nTPM
Lung	26.2 nTPM
Endometrium	26.0 nTPM
Bone marrow	25.0 nTPM
Skeletal muscle	22.1 nTPM
Esophagus	17.3 nTPM
Spleen	16.5 nTPM
PBMC	13.6 nTPM

Paneth cells	18.4 nTPM
Rectum	20.4 nTPM
Colon	19.7 nTPM
Small intestine	15.0 nTPM

Plasma cells	20.3 nTPM
Stomach	35.3 nTPM
Spleen	21.8 nTPM
Bone marrow	16.5 nTPM
Adipose tissue	15.5 nTPM
Esophagus	12.3 nTPM

Respiratory ciliated cells	28.2 nTPM
Lung	29.1 nTPM
Bronchus	27.3 nTPM

Smooth muscle cells	24.6 nTPM
Pancreas	61.3 nTPM
Ovary	32.5 nTPM
Breast	32.4 nTPM
Esophagus	27.9 nTPM
Heart muscle	23.0 nTPM
Endometrium	16.9 nTPM
Skeletal muscle	16.9 nTPM
Skin	16.0 nTPM
Bronchus	16.0 nTPM
Prostate	15.9 nTPM
Adipose tissue	12.0 nTPM

T-cells	27.0 nTPM
Colon	50.4 nTPM
Stomach	46.3 nTPM
Ovary	40.0 nTPM
Adipose tissue	35.8 nTPM
Liver	29.9 nTPM
Skin	29.0 nTPM
Kidney	28.7 nTPM
Spleen	26.1 nTPM
Breast	23.7 nTPM
PBMC	23.6 nTPM
Endometrium	22.3 nTPM
Bone marrow	20.5 nTPM
Esophagus	19.7 nTPM
Prostate	19.0 nTPM
Lung	18.2 nTPM
Skeletal muscle	17.2 nTPM
Lymph node	9.3 nTPM

Basal squamous epithelial cells	11.4 nTPM
Esophagus	11.4 nTPM

Cholangiocytes	21.5 nTPM
Liver	21.5 nTPM

Cone photoreceptor cells	12.5 nTPM
Eye	12.5 nTPM

Distal tubular cells	39.2 nTPM
Kidney	39.2 nTPM

Undifferentiated cells	18.9 nTPM
Small intestine	20.5 nTPM
Colon	18.6 nTPM
Rectum	17.5 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