Single cell type - CALHM2 - 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.	CALHM2
Gene descriptionⁱ Full gene name according to HGNC.	Calcium homeostasis modulator family member 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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.	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.	Fibroblasts - ECM organization (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 (Decidual stromal cells, Extravillous trophoblasts, Hofbauer cells, Vascular smooth muscle cells, Fibroblasts, Ovarian stromal cells, Lymphatic endothelial cells, Vascular endothelial cells, Pericytes, Leydig 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.	0.78
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.	Cell type enhanced (Vascular associated smooth muscle cell, Leukocyte, Endothelial cell)
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

Cell type enrichment

Single nuclei - Brain

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 (Stromal cells, Trophoblast cells, Mononuclear phagocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Vascular associated smooth muscle cell, Leukocyte, Endothelial cell)

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

CALHM2 is part of cluster 108 Fibroblasts - ECM organization with confidenceⁱ 1
348 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.
MFAP5	Microfibril associated protein 5	0.5436	108
ANGPT4	Angiopoietin 4	0.5431	110
CRTAP	Cartilage associated protein	0.5379	62
IGFBP5	Insulin like growth factor binding protein 5	0.5210	108
AIP	Aryl hydrocarbon receptor interacting protein	0.5194	97
MXRA8	Matrix remodeling associated 8	0.5151	108
GSC	Goosecoid homeobox	0.5028	108
GSN	Gelsolin	0.4961	108
MMP2	Matrix metallopeptidase 2	0.4954	108
IGFBP6	Insulin like growth factor binding protein 6	0.4950	108
CCN5	Cellular communication network factor 5	0.4869	108
FBLN2	Fibulin 2	0.4785	108
CCDC80	Coiled-coil domain containing 80	0.4736	108
CMTM3	CKLF like MARVEL transmembrane domain containing 3	0.4666	21
PLAC9	Placenta associated 9	0.4647	108

IMMUNE CELLS

CALHM2 is part of cluster 37 Monocytes & Neutrophils - Innate immune response with confidenceⁱ 0.98
275 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.
CCRL2	C-C motif chemokine receptor like 2	1.0000	37
SPNS1	Sphingolipid transporter 1 (putative)	1.0000	37
CKB	Creatine kinase B	1.0000	37
ACP2	Acid phosphatase 2, lysosomal	1.0000	37
TUBA1B	Tubulin alpha 1b	1.0000	37
PSMA4	Proteasome 20S subunit alpha 4	1.0000	37
CDK2AP1	Cyclin dependent kinase 2 associated protein 1	1.0000	37
ICAM4	Intercellular adhesion molecule 4 (Landsteiner-Wiener blood group)	1.0000	37
P2RX7	Purinergic receptor P2X 7	1.0000	37
GALE	UDP-galactose-4-epimerase	0.9762	37
RABGGTA	Rab geranylgeranyltransferase subunit alpha	0.9762	37
ADGRE2	Adhesion G protein-coupled receptor E2	0.9762	37
SNX24	Sorting nexin 24	0.9762	37
TPMT	Thiopurine S-methyltransferase	0.9762	37
ARRB1	Arrestin beta 1	0.9762	37