Single cell type - PMF1-BGLAP - 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.	PMF1-BGLAP
Gene descriptionⁱ Full gene name according to HGNC.	PMF1-BGLAP 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.	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.	Plasma cells - Plasma cell differentiation (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 (Salivary basal cells, Ovarian stromal cells, Endometrial luminal 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.	0.62
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 (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: Low cell type specificity

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

PMF1-BGLAP is part of cluster 67 Plasma cells - Plasma cell differentiation with confidenceⁱ 1
116 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.
RPL36A-HNRNPH2	RPL36A-HNRNPH2 readthrough	0.5136	67
CUTA	CutA divalent cation tolerance homolog	0.4960	67
JUN	Jun proto-oncogene, AP-1 transcription factor subunit	0.4790	20
NR4A1	Nuclear receptor subfamily 4 group A member 1	0.4703	103
CIRBP	Cold inducible RNA binding protein	0.4698	15
IGLC3	Immunoglobulin lambda constant 3 (Kern-Oz+ marker)	0.4688	67
FOSB	FosB proto-oncogene, AP-1 transcription factor subunit	0.4687	20
IGLC2	Immunoglobulin lambda constant 2	0.4680	67
IGHV3-13	Immunoglobulin heavy variable 3-13	0.4625	67
BGLAP	Bone gamma-carboxyglutamate protein	0.4526	67
U2AF1L4	U2 small nuclear RNA auxiliary factor 1 like 4	0.4470	67
IGLC7	Immunoglobulin lambda constant 7	0.4414	67
RPL10	Ribosomal protein L10	0.4391	15
IGHA1	Immunoglobulin heavy constant alpha 1	0.4389	67
IGHV7-4-1	Immunoglobulin heavy variable 7-4-1	0.4357	67

IMMUNE CELLS

PMF1-BGLAP is part of cluster 36 Eosinophils - Protein ubiquitination with confidenceⁱ 0.98
179 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.
SNAI3	Snail family transcriptional repressor 3	0.9762	36
MYH9	Myosin heavy chain 9	0.9524	36
RAB3GAP1	RAB3 GTPase activating protein catalytic subunit 1	0.9524	21
HOMEZ	Homeobox and leucine zipper encoding	0.9286	36
GNB1L	G protein subunit beta 1 like	0.9286	36
MFNG	MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0.9286	36
UBTD1	Ubiquitin domain containing 1	0.9286	36
C6orf52	Chromosome 6 open reading frame 52	0.9286	36
ARMC7	Armadillo repeat containing 7	0.9048	36
WIPI2	WD repeat domain, phosphoinositide interacting 2	0.9048	36
FBXO38	F-box protein 38	0.9048	36
CCN3	Cellular communication network factor 3	0.9048	36
KLHDC10	Kelch domain containing 10	0.9048	36
LAMP3	Lysosomal associated membrane protein 3	0.9048	3
NEURL2	Neuralized E3 ubiquitin protein ligase 2	0.9048	3