Table 1: Summary of proteins supported by RNAi or CRISPR screen experiments identified by SDREM from time-series bulk and single-cell SARS-CoV-2 expression data sets.
For each protein, we list RNA-seq experimental evidence [‘Bu’ for bulk, ‘Sc1’ (Calu3 cells) or ‘Sc2’ (human airway epithelium cells) for single-cell experiments, and ‘All’ for bulk and single-cell experiments], whether it is a known interactor of a SARS-CoV-2 protein and a brief description of the experimental impact on coronavirus load. Table enumerates each protein previously reported to affect coronavirus load in RNAi or CRISPR screen experiments for the set of proteins identified by SDREM from SARS-CoV-2 data (p values: 2.49e-4 for bulk data set; 9.28e-4 and 2.97e-4 for each single-cell data set, respectively). Proteins also listed in the top 1000 protein pairs identified by SDREM from either bulk or single-cell data sets are shown in boldface (p values: 1.52e-2 for bulk data; 8.97e-2 and 6.43e-3 for Sc1 and Sc2, respectively).
| Gene name | RNA-seq | SARS-CoV-2 interactor? | RNAi supported effect |
|---|---|---|---|
| POU3F2 | Bu | N | decreased IBV-CoV replication |
| UBE2I | Bu | N | decreased IBV-CoV replication |
| ATP6AP1 | Sc1 | Y | decreased SARS-CoV-2 replication |
| CAV2 | Sc1 | Y | decreased IBV-CoV replication |
| CSNK2A1 | Sc1 | N | decreased SARS-CoV replication |
| GBF1 | Sc2 | Y | decreased SARS-CoV-2 replication |
| NFKB1 | Sc2 | N | decreased MERS-CoV replication |
| TTC27 | Sc2 | Y | decreased SARS-CoV replication |
| SMARCA4 | Bu, Sc1 | N | conferred resistance to SARS-CoV-2 |
| NPC2 | Bu, Sc2 | Y | decreased SARS-CoV-2 replication |
| PISD | Bu, Sc2 | Y | decreased IBV-CoV replication |
| RAB7A | Bu, Sc2 | Y | affected MHV-CoV fusion decreased SARS-CoV-2 load |
| VPS39 | Bu, Sc2 | Y | affected MHV-CoV fusion |
| ACVR1 | Sc1, Sc2 | Y | decreased SARS-CoV replication |
| ACVR1B | All | Y | decreased SARS-CoV replication |
| ATM | All | Y | decreased SARS-CoV-2 load |
| ATP6V1A | All | Y | decreased SARS-CoV-2 replication |
| CAV1 | All | Y | decreased IBV-CoV replication |
| DYNC2H1 | All | Y | decreased MHV expression |
| EPHA2 | All | Y | decreased SARS-CoV replication |
| G3BP2 | All | Y | decreased SARS-CoV-2 load |
| MDH1 | All | Y | decreased IBV replication |
| RBX1 | All | Y | decreased IBV-CoV replication |
| SMAD3 | All | N | conferred resistance to SARS-CoV-2 |
| SMAD4 | All | N | conferred resistance to SARS-CoV-2 |