Table 2: 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 RNA-seq experimental evidence (‘Bu’ for bulk, ‘Sc’ for single-cell, and ‘Both’ for bulk and single-cell), 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: 6.32e–4 for bulk data; 2.50e–3 for single-cell data). 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: 7.70e–3 for bulk data; 8.28e–3 for single-cell data).
| Gene name | RNA-seq | SARS-CoV-2 interactor? | RNAi supported effect |
|---|---|---|---|
| PISD | Bu | Y | decreased IBV-CoV replication |
| POU3F2 | Bu | N | decreased IBV-CoV replication |
| RAB7A | Bu | Y | affected MHV-CoV fusion |
| decreased SARS-CoV-2 load | |||
| UBE2I | Bu | N | decreased IBV-CoV replication |
| VPS39 | Bu | Y | affected MHV-CoV fusion |
| ACVR1 | Sc | Y | decreased SARS-CoV replication |
| CAV2 | Sc | Y | decreased IBV-CoV replication |
| CSNK2A1 | Sc | N | decreased SARS-CoV replication |
| ACVR1B | Both | Y | decreased SARS-CoV replication |
| ATM | Both | Y | decreased SARS-CoV-2 load |
| CAV1 | Both | Y | decreased IBV-CoV replication |
| DYNC2H1 | Both | Y | decreased MHV expression |
| EPHA2 | Both | Y | decreased SARS-CoV replication |
| G3BP2 | Both | Y | decreased SARS-CoV-2 load |
| MDH1 | Both | Y | decreased IBV replication |
| RBX1 | Both | Y | decreased IBV-CoV replication |
| SMAD3 | Both | N | conferred resistance to SARS-CoV-2 |
| SMAD4 | Both | N | conferred resistance to SARS-CoV-2 |
| SMARCA4 | Both | N | conferred resistance to SARS-CoV-2 |