Multiscale Interactome Data -- Revised

<strong>Original GitHub Repository: </strong>https://github.com/snap-stanford/multiscale-interactome <strong>Forked GitHub Repository: </strong>https://github.com/callahantiff/multiscale-interactome/tree/development This repository stores a revised version of the original data that was used in the publication titled: Identification of disease treatment mechanisms through the multiscale interactome. As described in the original GitHub's Readme, the original data can be downloaded directly from: http://snap.stanford.edu/multiscale-interactome/data/data.tar.gz. <strong>Description of Original Data</strong> <strong>Drug-Protein (n=8,568):</strong> Source(s): DrugBank (<code>v5.1.1; 2018</code>; <code>drugbank_approved_target_uniprot_links.csv</code>) Drug Repurposing Hub (<code>September 2018</code>) Processing: map Uniprot to Entrez gene using HUGO (October 2018) and drug ids to DrugBank ids Filtering: Filter proteins to only keep those that appear in the Protein-Protein edge set. <strong>Disease-Protein (n=25,212):</strong> Source(s): DisGeNet (<code>March 2018</code>) Filtering: only keep only expert curated gene-disease associations. (1) exclude disease-gene relationships that are inferred, based on orthology, animal models, or literature mining; (2) remove therapeutic disease-gene associations; and (3) remove disease-gene relationships that do not appear in the Protein-Protein edge set. <strong>Protein-Protein (n=387,626):</strong> Source(s): BioGRID (<code>v3.5.178</code>; <code>November 2019</code>; <code>BIOGRID-ORGANISM-Homo_sapiens-3.5.178.tab</code>) Database of Interacting Proteins (<code>February 2017</code>; <code>Hsapi20170205.txt</code>). Include all experimental methods Human Reference Protein Interactome Mapping Project. Four networks derived from high-throughput yeast two hybrid assays. Menche 2015 (PMID:25700523). Compiles different types of physical protein-protein interactions. Processing: Map protein ids to Entrez gene ids using HUGO (sources 1-2 only) Filtering: only human proteins with physical interactions and direct experimental evidence (no genetic/indirect) <strong>Protein-Biological Process (n=34,777):</strong> Source(s): Gene Ontology (human; <code>February 2018</code>) Processing: use master ids provided by GOATOOLS (<code>v0.8.4</code>) Filtering: only allow: EXP, IDA, IMP, IGI, HTP, HDA, HMP, HGI. Exclude any protein-biological functions inferred from: physical interactions, gene expression patterns, phylogenetically inferred annotations or computational analyses, automatic annotations (i.e., based on author statements, curator inference, electronic annotation), and those with no biological data <strong>Biological Process-Biological Process (n=22,545):</strong> Source(s): Gene Ontology (human; <code>February 2018</code>) + Gene Ontology Plus (human version; <code>July 2020</code>) Filtering: Allow following relationship types: regulates, positively regulates, negatively regulates, part of, is a. Only consider BPs associated with at least one drug target or disease protein (directly or through children) ⚠️ <strong>Updates to Original Implementation</strong> ⚠️ <em>Modifications to Original Data and Code</em> Ensured every entry had a valid identifier and label Reconciled duplicate gene entries (i.e., gene identifiers that had been merged) Changed genes are listed in: <code>resources/data/updated_gene_identifiers.xlsx</code>