Table 1.
Datasets tested using the GESS online tool and results
| Study | RNAi (species) | Phenotype | No. active siRNA | Statistically significant OT gene |
|---|---|---|---|---|
| A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability [16] |
shRNA (hs) |
Ionizing radiation sensitivity |
850 |
ZNF480 SH3BP2 |
| Ionizing radiation sensitivity (validated) |
114 |
None |
||
| Ionizing radiation resistance |
1080 |
None |
||
| An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor [17] |
siRNA (hs) |
Genes involved in spindle assembly checkpoint (Dharmacon library) |
308 |
MAD2L1 |
| Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2 [18] |
siRNA (hs) |
Genes involved in TGF-β signaling (Sloan Kettering Inst. In house library) |
409 |
TGFBR2 |
| Genome-wide siRNA screen identifies SMCX, EP400 and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression [19] |
siRNA (hs) |
Genes that contribute to the repression of the HPV LCR. (Dharmacon library) |
511 |
None |
| A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response [12] |
siRNA (hs) |
Regulator of homologous recombination (Dharmacon library) |
510 |
Rad51 |
| Regulator of homologous recombination (Ambion library) |
187 |
None |
||
| Kinase requirements in human cells: I. Comparing kinase requirements across various cell types [20] |
TRC shRNA (hs) |
Essential kinases in HeLa and 293 T cell lines. |
110 |
None |
| A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Array Viral High-Content Screen [21] |
TRC shRNA (hs) |
Genes required for mitotic progression and proliferation for HT29 cell line |
161 |
None |
| Highly parallel identification of essential genes in cancer cells [22] |
TRC shRNA (hs) |
Essential genes for 12 cancer cell lines |
182 |
None |
| Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer [23] |
TRC shRNA (hs) |
Essential genes specifically for Ovarian cell lines |
~1500 (top ~3%) |
None |
| Essential genes specifically for Colon cell lines |
~1500 (top ~3%) |
None |
||
| Essential genes specifically for Pancreas cell lines |
~1500 (top ~3%) |
None |
||
| Essential genes specifically for Esophageal Squamous cell lines |
~1500 (top ~3%) |
TACO1 |
||
| Depleting gene activities in early Drosophila embryos with the "maternal-Gal4-shRNA" system [24] |
shRNA (dm) |
Abnormal embryonic phenotypes |
79 |
None |
| A regulatory network of Drosophila germline stem cell self-renewal [25] | shRNA (dm) | Abnormal embryonic phenotypes | 329 | None |
Note: The results presented here were obtained using the following parameters: “3’UTR” as genomic region, “antisense/guide” as strand to use, “7” as seed sequence length. The shRNA libraries from The RNAi Consortium (TRC) were trimmed by 2 bp.