Table 2.
Summary of the 12 drug lists generated from all repurposing pipelines
| Drug list name | Source DATA | Drug DB | Main pipeline methods and tools | Description |
|---|---|---|---|---|
| Tr1 | RNA-Seq—Series 1, 2 and 5, 6, 7 | LINCS L1000 | Connectivity Map, L1000CDS2, L1000FWD | Drugs aiming at reversing the gene expression profile induced by COVID-19 |
| TrC1 | RNA-Seq—Series 1, 2 and 5, 6, 7 | Drug Matrix (GSE5992) | CREEDS | |
| Tr2 | RNA-Seq—Series 15 | LINCS L1000 | Connectivity Map, L1000CDS2, L1000FWD | |
| TrC2 | RNA-Seq—Series 15 | Drug Matrix (GSE5992) | CREEDS | |
| Tr3 | RNA-Seq—BALF | LINCS L1000 | Connectivity Map, L1000CDS2, L1000FWD | |
| TrC3 | RNA-Seq—BALF | Drug Matrix (GSE5992) | CREEDS | |
| Tr4 | RNA-Seq—PBMC | LINCS L1000 | Connectivity Map, L1000CDS2, L1000FWD | |
| TrC4 | RNA-Seq—PBMC | Drug Matrix (GSE5992) | CREEDS | |
| GW | GWAS | DGIdb | Phenoscanner | Drugs targeting host proteins from genes with significant SNP–phenotypic association with COVID-19 |
| HPH | PPI, NCBI | DrugBank | In-house methods | Drugs targeting host proteins found to interact with SARS-CoV-2 proteins and/or other pathogens |
| HPAV | PPI, NCBI | DrugBank | In-house methods | Drugs targeting pathogen proteins—direct antiviral activity |
| TaxAV | NCBI | DrugBank | In-house methods |