Single cell type - CKLF-CMTM1 - 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.	CKLF-CMTM1
Gene descriptionⁱ Full gene name according to HGNC.	CKLF-CMTM1 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.	Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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.	T-cells - T-cell receptor (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 (Late spermatids, Sertoli cells, Collecting duct cells, Early spermatids)
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.	0.95
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 transcript 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: Cell type enhanced (Late spermatids, Sertoli cells, Collecting duct cells, Early spermatids)

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

CKLF-CMTM1 is part of cluster 7 T-cells - T-cell receptor with confidenceⁱ 1
246 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.
TRBV13	T cell receptor beta variable 13	0.7433	7
TRBV6-7	T cell receptor beta variable 6-7 (non-functional)	0.7157	7
TRBV10-1	T cell receptor beta variable 10-1	0.7133	7
TRGV1	T cell receptor gamma variable 1 (non-functional)	0.7123	7
TRBV10-2	T cell receptor beta variable 10-2	0.7115	7
TRBV4-1	T cell receptor beta variable 4-1	0.7074	7
TRBV7-7	T cell receptor beta variable 7-7	0.7063	7
MAD1L1	Mitotic arrest deficient 1 like 1	0.7056	7
TRGV2	T cell receptor gamma variable 2	0.7008	7
TRAV22	T cell receptor alpha variable 22	0.6981	7
TRBJ1-6	T cell receptor beta joining 1-6	0.6979	7
TRAV21	T cell receptor alpha variable 21	0.6953	7
TRGV8	T cell receptor gamma variable 8	0.6939	7
TRBV4-2	T cell receptor beta variable 4-2	0.6937	7
TRBJ2-7	T cell receptor beta joining 2-7	0.6934	7

IMMUNE CELLS

CKLF-CMTM1 is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.51
504 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.
DYNC1LI2	Dynein cytoplasmic 1 light intermediate chain 2	0.9762	28
SOD2	Superoxide dismutase 2	0.9762	4
TMEM120A	Transmembrane protein 120A	0.9762	4
CXorf38	Chromosome X open reading frame 38	0.9762	35
GP1BA	Glycoprotein Ib platelet subunit alpha	0.9762	4
S100A11	S100 calcium binding protein A11	0.9762	21
SYNJ1	Synaptojanin 1	0.9762	35
ACSL1	Acyl-CoA synthetase long chain family member 1	0.9762	4
NRBF2	Nuclear receptor binding factor 2	0.9762	4
ARL3	ADP ribosylation factor like GTPase 3	0.9762	4
IFI6	Interferon alpha inducible protein 6	0.9762	28
SRGN	Serglycin	0.9762	21
NUP98	Nucleoporin 98 and 96 precursor	0.9762	4
AQP9	Aquaporin 9	0.9762	4
PTGS2	Prostaglandin-endoperoxide synthase 2	0.9762	4