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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.
Assigned HPA protein class(es) for the encoded protein(s).
Enzymes Metabolic proteins
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, Intracellular
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.
Monocytes - Innate immune response (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.
Low cell type specificity
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.
0.34
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.
Low cell type specificity
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
Overview of the different datasets included in the Single Cell resource.
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: Low cell type specificity
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
A summary of normalized single nuclei RNA (nTPM) from the brain single nuclei. Color-coding is based on cell type groups (as defined in the single cell type data representing the whole body), in this case separated into the main cell categories of neuron, glial cells, endothelial cells, fibroblasts and muscle cell (vascular smooth muscle cells and pericytes).
RNA brain cluster 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
The RNA data was used to cluster genes according to their expression across samples. The resulting clusters have been manually annotated to describe common features in terms of function and specificity. The annotation of the cluster is displayed together with a confidence score of the gene's assignment to the cluster. The confidence is calculated as the fraction of times the gene was assigned to this cluster in repeated calculations and is reported between 0 to 1, where 1 is the highest possible confidence. The clustering results are shown in a UMAP, where the cluster this gene was assigned to is highlighted as a colored area in which most of the cluster genes reside. A table shows the 15 most similar genes in terms of expression profile.
SINGLE CELL TYPE
PAPOLG is part of cluster 29Monocytes - Innate immune response with confidencei
Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. A confidence of 1 indicates that the gene was assigned to this cluster in all repeated clusterings.
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.
PAPOLG is part of cluster 35Neutrophils - Protein binding with confidencei
Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. A confidence of 1 indicates that the gene was assigned to this cluster in all repeated clusterings.
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.