†Score refer to the CMap score. It represents the level of similarity between transcriptional effects induced by BCG and each of the compounds.

‡ Validation refers to the presence of any supporting evidence from the biomedical literature that the predicted BCG mimics have any antiviral activities. Antiviral means there is evidence that the compound is used as or has antiviral activity; SARS-CoV-2 means that the compound should antiviral activity against SARS-CoV-2; Corona viruses means that the compound showed antiviral activity against corona viruses other than SARS-CoV-2.

§ COVID-19 CT: there is evidence that the compound is being tested in clinical trials for COVID-19. There are 12 Studies found for Ruxolitinib in COVID-19 on clinicaltrials.gov.

Figure 1. Workflow for drug and vaccine repurposing. ① A gene signature is identified/derived and a consensus gene signature is prioritized, all genes are nomenclated according to HUGO Gene Nomenclature Committee (HGNC). ② The consensus gene signature is used to query the CMap to identify positive connections capable of producing gene signatures similar to BCG-CGS. ③ Prioritize genes and compounds that induce transcriptional changes similar to those induced by BCG: A) key hubs predicted by causal reasoning; B) Positive genes and compound connections from the connectivity map. ④ Prioritize top enriched pathway map explaining the biological effects of BCG (gene annotations on the pathway map are assigned by Clarivate Analytics, IFN-gamma is an alias for INFG, GM-CSF is an alias for CSF2, MIP-1-alpha is an alias for CCL3).

Figure 2. BCG’s consensus gene signature (BCG-CGS) and highly enriched pathways. (A) A heat map of the log₂FC of the gene expression for differentially expressed genes representing BCG’s consensus gene signature. Upregulated genes have positive log₂FC denoted in red color, and down regulated genes have negative values for log₂FC denoted in blue color. (B) Core network for BCG-CGS showing highly connected genes in BCG-CGS, deleting all singleton genes. Nodes are color-coded using a split pie chart coloring scheme indicating pathway/gene set contribution to each node from the top 5 most enriched pathways/gene lists. All details about pathway/gene set ID are found in Table S2 (Supporting Information).

­­­­­Figure 3. High-confidence expanded network for BCG-CGS. Nodes are color-coded using a split pie chart coloring scheme indicating pathway/gene set contribution to each node from the top 5 most enriched pathways/gene lists. Core network is composed of genes in the BCG-CGS that are not singletons. Step 1 expansion, added 10 additional nodes (i.e., genes) to the core network. Step 2 expansion, added another 10 nodes for the first expansion. Step 3 expansion, added another 10 nodes to the second expansion. Expansions were performed to see which pathways remained most statistically significant, and therefore are considered high confidence pathways.

Figure 4. (A) A venn diagram showing overlaps between BCG genetic mimics and key hubs with SARS-CoV-2 and Corona viruses interactomes. (B) Top “pathway map” with the highest level of enrichment by genes in BCG-CGS. This map is generated using MetaCore from Clarivate Analytics. Red thermometers indicate genes overexpressed in response to BCG treatment, and the hight of the red bars is representative of the differential gene expression level (i.e., log₂ values of the fold change). The numbers under the thermometers 1- 5 refer to the experiment number: 1) gene expression on day 1 in response to BCG vaccination to a BCG-naïve population on day 1; 2) gene expression on day 1 in response to BCG re-vaccination to a previously vaccinated population; 3) gene expression on day 1 in response to BCG vaccination to a BCG-naïve population on day 14; 4) gene expression on day 14 in response to BCG re-vaccination to a previously vaccinated population, and 5) positive connections from the connectivity map, and the red bar in the thermometer number 5 represents presence of the gene only.