Single cell type - ATP5MF-PTCD1 - 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.	ATP5MF-PTCD1
Gene descriptionⁱ Full gene name according to HGNC.	ATP5MF-PTCD1 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.	1

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.	Oligodendrocyte precursor - 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.	Group enriched (Microglial cells, Astrocytes, Oligodendrocyte precursor cells, Oligodendrocytes, Inhibitory neurons, Excitatory neurons, Melanocytes)
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.	0.89
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 (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: Group enriched (Microglial cells, Astrocytes, Oligodendrocyte precursor cells, Oligodendrocytes, Inhibitory neurons, Excitatory neurons, Melanocytes)

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

ATP5MF-PTCD1 is part of cluster 76 Oligodendrocyte precursor - Unknown function with confidenceⁱ 1
210 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.
LSAMP	Limbic system associated membrane protein	0.7569	47
CDH4	Cadherin 4	0.7466	47
WWOX	WW domain containing oxidoreductase	0.7387	76
TOMM6	Translocase of outer mitochondrial membrane 6	0.7359	47
OR9A4	Olfactory receptor family 9 subfamily A member 4	0.7128	47
SPOUT1	SPOUT domain containing methyltransferase 1	0.7117	47
ZNF559-ZNF177	ZNF559-ZNF177 readthrough	0.7100	69
UTP14C	UTP14C small subunit processome component	0.6889	69
NAV2	Neuron navigator 2	0.6831	76
BCL2L2-PABPN1	BCL2L2-PABPN1 readthrough	0.6808	69
TMEM265	Transmembrane protein 265	0.6560	47
ZSWIM5	Zinc finger SWIM-type containing 5	0.6375	69
CHURC1-FNTB	CHURC1-FNTB readthrough	0.6363	76
LINGO1	Leucine rich repeat and Ig domain containing 1	0.6305	76
PRKN	Parkin RBR E3 ubiquitin protein ligase	0.6295	8

IMMUNE CELLS

ATP5MF-PTCD1 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.94
458 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.
COX5A	Cytochrome c oxidase subunit 5A	0.9762	13
HSD17B10	Hydroxysteroid 17-beta dehydrogenase 10	0.9762	13
DUS3L	Dihydrouridine synthase 3 like	0.9762	13
ENSG00000255639	Novel protein	0.9524	33
ARMC6	Armadillo repeat containing 6	0.9524	33
MPV17	Mitochondrial inner membrane protein MPV17	0.9524	13
CPSF3	Cleavage and polyadenylation specific factor 3	0.9524	13
ITPA	Inosine triphosphatase	0.9524	13
ERAL1	Era like 12S mitochondrial rRNA chaperone 1	0.9524	13
ATG4B	Autophagy related 4B cysteine peptidase	0.9524	13
MDH2	Malate dehydrogenase 2	0.9524	13
PIGF	Phosphatidylinositol glycan anchor biosynthesis class F	0.9524	13
NDUFA9	NADH:ubiquinone oxidoreductase subunit A9	0.9286	13
HDAC3	Histone deacetylase 3	0.9286	12
TRAPPC2L	Trafficking protein particle complex subunit 2L	0.9286	13