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.
HUMAN PROTEIN ATLAS INFORMATION
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
or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.
Secreted to blood
All genes belonging to the secretome have been classified according to function based on Uniprot molecular function and biological processes keywords.
The functional annotations are prioritized according to the following hierarchy: Blood coagulation, Complement pathway, Acute phase, Cytokine, Hormone, Neuropeptide, Growth factor, Receptor, Transport, Developmental protein, Defence, Enzyme, Enzyme inhibitor, Transcription, Immunity, Cell adhesion, Other and each gene is assigned a single function.
The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search.
Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.
Proximity extension assayi
Detection or not of the gene in blood, based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years.
PROTEIN CONCENTRATION IN BLOOD - IMMUNOASSAYi
Plasma or serum concentrations of the genes annotated as actively secreted to blood. Up to three values for each gene were compiled from a literature search limited to studies where the protein concentration was determined using an antibody-based assay such as enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) or immunoturbidimetry (IT).
PROTEIN CONCENTRATION IN PLASMA - MASS SPECTROMETRYi
The protein concentration in blood is quantified by mass spectrometry-based plasma proteomics and estimated from spectral counts in a publicly available data set obtained from the PeptideAtlas.
Detected in plasma by mass spectrometry
17 mg/L, PeptideAtlas
PROTEIN DETECTED IN PLASMA - PROXIMITY EXTENSION ASSAYi
The protein profiling results based on proximity extension assays (Olink) for a longitudinal wellness study covering 76 individuals with three visits during two years. Protein expression levels are reported as Normalized Protein eXpression (NPX).