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In SupData.xlsx, there are 11 sheets:

  1. D_mapping: drug index, PubChem identifier, synonyms, and IUPAC name
  2. P_mapping: Protein index, GeneID, and gene symbol
  3. SE_mapping: Side effect index and name
  4. SE_MeSH_category: Side effect index and name, as well as MeSH category symbol and name
  5. SE_cluster: Side effect index and cluster name
  6. SE-GO_adj_with_#gene: Each row is a side effect, and each column is a GO item. The value in each cell is the number of genes identified by explainer for the side effect (row) in the GO(column).
  7. sepsis_hi: Explanations for sepsis with high PPIU
  8. sepsis_low: Explanations for sepsis with low PPIU
  9. cluster_enrich_mesh: MeSH category, cluster center, P-value of over-representation of MeSH category based on Fisher's exact test, odds ratio from Fisher's exact test, cluster size, Benjamini-Hochberg adjusted P-value, and category name
  10. CTD_permutation_test:
    • side effect index and name
    • permutation P-value for precision and Jaccard index
    • precision
    • Jaccard index
    • mean precision and Jaccard index of 10,000 random explanations
    • random model: nongo_strong (entire subgraph, not necessarily GO-enriched; preserve target and non-target numbers), nongo_weak (entire subgraph, not necessarily GO-enriched; not preserving target and non-target numbers), go_strong (subgraph with GO-enriched genes only, preserve target and non-target numbers), go_weak (subgraph wit GO-enriched genes only, not preserving target and non-target numbers)
    • number of predicted proteins, genes in CTD associated with the side effect (disease), target genes and non-target genes in the explanation, and random explanations
    • 100% * (Precision_predicted - Mean(Precision_random)) / Mean(Precision_random)
    • 100% * (Jaccard_predicted - Mean(Jaccard_random)) / Mean(Jaccard_random)
  11. cluster_enrich_GO: Gene Ontology term, cluster center (exemplar), P-value of enrichment of GO term in cluster and odds ratio based on Fisher's exact test, cluster size and Benjamini-Hochberg adjusted P-value

Beside, the APRILE's explanations for the top 200 polypharmacy side effect predictions (ranked by predicted probability score) in training set are provided in exp_top200_train.csv.