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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.
All genes with at least one predicted secreted isoform have been annotated and classified with the aim to determine if the corresponding protein(s) are:
secreted into blood
locally secreted
or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.
A gene is classified as upregulated in a disease if the average concentration of all samples of that disease is significantly higher (adj P-value<0.05) than the average concentration of samples of all diseases as measured by PEA . For gender specific diseases the analysis includes only samples corresponding to the same gender from the other diseases.
No
Disease prediction model (PEA)i
The disease(s) the gene is associated with and able to predict according to glmnet prediction models. To be included the gene has to be upregulated according to differential expression analysis and have more than 50% overall importance as indicated by the prediction models.
No
PEA - PROTEIN CONCENTRATIONS IN THE PAN-CANCER COHORTi
Relative plasma concentrations of proteins in blood from patients having different types of cancer measured by proximity extension assay (PEA).
MS - PROTEIN CONCENTRATIONS IN THE PAN-CANCER COHORTi
Plasma concentrations of proteins in blood from patients having different types of cancer measured by quantitative mass spectrometry (MS) using isotope dilution strategies based on the addition of recombinant protein fragment standards.
The Human Protein Atlas project is funded
