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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.
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
IMMUNE CELL SECTION SUMMARY
Immune cell type expression clusteri
The RNA data is used to cluster genes according to their expression across immune cells. 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.
Non-specific - Mitochondria (mainly)
Immune cell type 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
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.
0.09
Immune cell type distributioni
The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected.
Detected in all
Immune cell lineage specificityi
The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: lineage enriched, group enriched, lineage enhanced, low lineage specificity and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells.
Low lineage specificity
Immune cell lineage distributioni
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.
Detected in all
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.
ATG4B is part of cluster 13Non-specific - Mitochondria 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.
The Human Protein Atlas project is funded
