Single cell type - GCOM1 - 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.	GCOM1
Gene descriptionⁱ Full gene name according to HGNC.	GCOM1, MYZAP-POLR2M combined locus
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.	4

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.	Glandular & Luminal cells - 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.	Cell type enhanced (Cardiomyocytes, Glandular and luminal cells, Paneth 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.	0.75
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 (Upper rhombic lip, Lower rhombic lip)
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.	Immune cell enhanced (naive CD4 T-cell, naive B-cell)
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

Single nuclei - Brain

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 (Cardiomyocytes, Glandular and luminal cells, Paneth cells)

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Upper rhombic lip, Lower rhombic lip)

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: Immune cell enhanced (naive CD4 T-cell, naive B-cell)
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

GCOM1 is part of cluster 37 Glandular & Luminal cells - Unknown function with confidenceⁱ 1
334 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.
MYZAP	Myocardial zonula adherens protein	0.6039	68
LIMS3	LIM zinc finger domain containing 3	0.5526	37
NFE2L1	NFE2 like bZIP transcription factor 1	0.5446	68
PTPN3	Protein tyrosine phosphatase non-receptor type 3	0.5419	37
TSPAN12	Tetraspanin 12	0.5291	3
DAND5	DAN domain BMP antagonist family member 5	0.5242	68
KIF1C	Kinesin family member 1C	0.5220	32
C2CD4A	C2 calcium dependent domain containing 4A	0.5216	37
NALF2	NALCN channel auxiliary factor 2	0.5205	68
MRPL33	Mitochondrial ribosomal protein L33	0.5193	68
CCDC9B	Coiled-coil domain containing 9B	0.5167	45
LIMS4	LIM zinc finger domain containing 4	0.5156	37
PDLIM5	PDZ and LIM domain 5	0.5093	68
CNKSR3	CNKSR family member 3	0.5082	37
PAEP	Progestagen associated endometrial protein	0.5016	37

IMMUNE CELLS

GCOM1 is part of cluster 14 Non-specific - Unknown function with confidenceⁱ 0.34
292 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.
QTRT2	Queuine tRNA-ribosyltransferase accessory subunit 2	0.9762	14
RPAP3	RNA polymerase II associated protein 3	0.9524	14
ADD2	Adducin 2	0.9524	14
RERE	Arginine-glutamic acid dipeptide repeats	0.9524	14
CD83	CD83 molecule	0.9524	14
TMEM131L	Transmembrane 131 like	0.9524	40
MYZAP	Myocardial zonula adherens protein	0.9286	2
TBC1D16	TBC1 domain family member 16	0.9286	40
IFI16	Interferon gamma inducible protein 16	0.9286	14
SH2B2	SH2B adaptor protein 2	0.9286	2
NAA50	N-alpha-acetyltransferase 50, NatE catalytic subunit	0.9286	14
MTMR4	Myotubularin related protein 4	0.9286	14
CCNE1	Cyclin E1	0.9286	40
SLC25A43	Solute carrier family 25 member 43	0.9286	40
IGF2BP3	Insulin like growth factor 2 mRNA binding protein 3	0.9048	2