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KEY RESOURCES TABLE
REAGENT or RESOURCE SOURCE
Software and Algorithms
The R Project for Statistical Computing
The MathWorks, Inc.
CONTACT FOR REAGENT AND RESOURCE SHARING
Further information and requests for resources should be directed to and will be fulfilled by the Lead Contact, Jens Nielsen ([email protected] chalmers.se).
Definition of the secretome and SP genes
The list of proteins comprising the classically secreted secretome was obtained via UniProt (uniprot.org) (Bateman et al., 2017). Beginning with the entire human proteome (UP000005640), proteins were filtered to include those labeled as ‘‘UniProtKB/Swiss-Prot (reviewed),’’ with a subcellular location of ‘‘Secreted,’’ and PTM/Processing of ‘‘Signal peptide,’’ yielding 1,838 unique UniProt entries. The associated Entrez gene IDs and gene names were mapped to Ensembl IDs (GRCh38.p12), where those that did not map were excluded, and duplicated entries were removed, resulting in a secretome of 1,816 unique genes when analyzing TCGA data. For analyses also involving GTEx samples, genes absent from the that dataset were excluded, yielding a secretome comprised of 1,810 genes.
SP (signal peptide) genes were defined and generated in the same way as the secretome, except without the requirement for a subcellular location of ‘‘Secreted.’’ This resulted in a set of 3,491 SP genes, of which 3,111 had associated differential expression data (TCGA primary tumor versus paired normal).
The experimentally-derived secretome