| GR00053-A |
23534 |
NM_012470 |
TNPO3 |
np |
sp |
Increased gamma-H2AX phosphorylation |
|
no |
group 4 |
Genome stability |
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. |
Paulsen et al. |
2009 |
19647519 |
Cell line |
HeLa |
gamma-H2AX phosphorylation and DNA content |
Fluorescence |
siARRAY human genome siRNA library |
Genome-wide |
siRNA |
p-value |
Complex criteria |
Confidence groupings from 4 to 1 (highest level of confidence in group 4) |
GR00054-A |
23534 |
NM_012470 |
TNPO3 |
np |
0.784 |
none |
|
no |
|
Combinatorial effect with paclitaxel |
Synthetic lethal screen identification of chemosensitizer loci in cancer cells. |
Whitehurst et al. |
2007 |
17429401 |
Cell line |
NCI-H1155 |
Viability (synthetic lethal) |
ATP level |
# G-005000-01 |
Genome-wide |
siRNA |
Paclitaxel/control ratio |
Complex criteria |
Additional information about 87 high-confidence hits |
GR00056-A |
23534 |
NM_012470 |
TNPO3 |
np |
1.284 |
none |
|
no |
|
Melanogenesis |
Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. |
Ganesan et al. |
2008 |
19057677 |
Cell line |
MNT-1 |
Melanin protein expression and viability |
Absorbance and luminescence |
rp |
Genome-wide |
siRNA |
Normalized absorbance ratio |
> 2 standard deviations below mean |
Additional information about a secondary screen (retest to determine false-positive rate) |
GR00057-A-1 |
23534 |
NM_012470 |
TNPO3 |
M-019949-00 |
1.46 |
none |
|
no |
|
Wnt/beta-catenin pathway regulation (1) |
A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. |
Tang et al. |
2008 |
18621708 |
Cell line |
HeLa |
Wnt pathway reporter |
Luminescence |
Human siArray siRNA library |
Genome-wide |
siRNA |
Z-score |
> 4 |
Screen without Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries). |
GR00057-A-2 |
23534 |
NM_012470 |
TNPO3 |
M-019949-00 |
sp |
none |
|
no |
|
Wnt/beta-catenin pathway regulation (2) |
A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. |
Tang et al. |
2008 |
18621708 |
Cell line |
HeLa |
Wnt pathway reporter |
Luminescence |
Human siArray siRNA library |
Genome-wide |
siRNA |
Complex, SP |
Complex criteria |
Screen with Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries). |
GR00098-A-1 |
23534 |
ENSG00000064419 |
TNPO3 |
ENSG00000064419 |
sp |
none |
|
no |
|
Cell division (1) |
Genome-scale RNAi profiling of cell division in human tissue culture cells. |
Kittler et al. |
2007 |
17994010 |
Cell line |
HeLa |
Cell number and DNA content |
Laser scanning cytometry |
rp |
Genome-wide |
esiRNA |
Complex, sp |
Complex criteria |
|
GR00133-A-1 |
23534 |
23534 |
TNPO3 |
np |
0.463098 |
none |
|
no |
|
Salmonella enterica subspecies 1 serovar Typhimurium invasion (1) |
RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. |
Misselwitz et al. |
2011 |
21407211 |
Cell line |
HeLa |
Gentamycin protection invasion assay |
Fluorescence |
Druggable genome library V2.0 |
Druggable genes |
siRNA |
log2 median |
Complex criteria |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
20147 |
27.88 |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
20147 |
np |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
20241 |
70.75 |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
20241 |
51.55 |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
108368 |
1 |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00149-A-1 |
23534 |
23534 |
TNPO3 |
108368 |
-43.39 |
none |
|
no |
|
Ciliogenesis and cilium length (1) |
Functional genomic screen for modulators of ciliogenesis and cilium length. |
Kim et al. |
2010 |
20393563 |
Cell line |
htRPE |
Smoothed protein expression |
Fluorescence |
Human druggable genome siRNA library V3.1 |
Druggable genes |
siRNA |
Normalized percent inhibition |
> 1.5 OR < -1.5 standard deviations from mean |
|
GR00151-A-1 |
23534 |
ENSG00000064419 |
TNPO3 |
np |
-1.093 |
none |
|
no |
|
Homologous recombination DNA double-strand break repair (HR-DSBR) (1) |
A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. |
SÅ‚abicki et al. |
2010 |
20613862 |
Cell line |
HeLa |
(HR-DSBR) DR-GFP reporter |
Flow cytometry |
Custom-made |
Genome-wide |
esiRNA |
Z-score |
< -2 OR > 2 |
|
GR00163-A-1 |
23534 |
23534 |
TNPO3 |
M-019949-00 |
23 |
Decreased p24 protein expression |
|
yes |
|
HIV-1 infection (1) |
Identification of host proteins required for HIV infection through a functional genomic screen. |
Brass et al. |
2008 |
18187620 |
Cell line |
TZM-bl |
p24 protein expression |
Fluorescence |
siARRAY siRNA Library |
Genome-wide |
siRNA |
Percentage of infected cells |
> |
|
GR00180-A-1 |
23534 |
23534 |
TNPO3 |
PL-50055 |
0.884 |
none |
|
no |
|
Hepatitis C virus replication (1) |
A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. |
Tai et al. |
2009 |
19286138 |
Cell line |
Huh7/Rep-Feo |
HCV replicon RNA copy number |
Luminescence |
siARRAY Human Genome siRNA Library |
Genome-wide |
siRNA |
q-value |
Complex criteria |
|
GR00184-A-1 |
23534 |
NM_012470 |
TNPO3 |
M-019949-00 |
-0.440802686486771 |
none |
|
no |
|
Self-renewal and pluripotency in human embryonic stem cells (1) |
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. |
Chia et al. |
2010 |
20953172 |
Cell line |
hESC H1 |
POU5F1 protein expression |
Fluorescence |
SMARTpool siRNA library |
Genome-wide |
siRNA |
Z-score |
< -2 |
|
GR00196-A-1 |
23534 |
ENSG00000064419 |
|
np |
sp |
none |
|
no |
|
TP53 interactions (1) |
A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. |
Krastev et al. |
2011 |
21642980 |
Cell line |
HCT116 ( wildtype and TP53 knockout) |
TP53 protein expression and viability |
Fluorescence |
rp |
Genome-wide |
esiRNA |
Complex, sp |
Complex criteria |
|
GR00197-A-1 |
23534 |
23534 |
TNPO3 |
M-019949-00 |
0.489276007 |
none |
|
no |
|
Human papillomavirus oncogene expression regulation (1) |
Genome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. |
Smith et al. |
2010 |
20133580 |
Cell line |
C33A/BE2/18LCR c4 |
HPV18 LCR reporter activity |
Luminescence |
Human siGENOME SMARTpool library |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5 |
GR00209-A-1 |
23534 |
NM_012470 |
TNPO3 (Trn-SR) |
np |
np |
none |
|
yes |
|
Ribosome biogenesis (1) |
A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. |
Wild et al. |
2010 |
21048991 |
Cell line |
HeLa |
Rps2 protein expression |
Fluorescence |
np |
Selected genes |
siRNA |
Average relative rank from > |
> 0.2 |
|
GR00209-A-2 |
23534 |
NM_012470 |
TNPO3 (Trn-SR) |
np |
np |
none |
|
yes |
|
Ribosome biogenesis (2) |
A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. |
Wild et al. |
2010 |
21048991 |
Cell line |
HeLa |
Enp1 protein expression |
Fluorescence |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
|
GR00209-A-3 |
23534 |
NM_012470 |
TNPO3 (Trn-SR) |
np |
np |
none |
|
no |
|
Ribosome biogenesis (3) |
A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. |
Wild et al. |
2010 |
21048991 |
Cell line |
HeLa |
Rpl29 protein expression |
Fluorescence |
np |
Selected genes |
siRNA |
Average relative rank from > |
> 0.25 |
|
GR00226-A |
23534 |
23534 |
TNPO3 |
TNPO3_siRNA_1 |
0.0752 |
Decreased HIV-1 infection |
|
yes |
|
HIV-1 infection |
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. |
König et al. |
2008 |
18854154 |
Cell line |
293T |
VSV-G HIV-1 reporter and viability |
Luminescence |
np |
Genome-wide |
siRNA |
Median evidence score |
Complex criteria |
Additional information about MLV and AAV infection screens |
GR00226-A |
23534 |
23534 |
TNPO3 |
TNPO3_siRNA_2 |
0.0803 |
Decreased HIV-1 infection |
|
yes |
|
HIV-1 infection |
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. |
König et al. |
2008 |
18854154 |
Cell line |
293T |
VSV-G HIV-1 reporter and viability |
Luminescence |
np |
Genome-wide |
siRNA |
Median evidence score |
Complex criteria |
Additional information about MLV and AAV infection screens |
GR00236-A-1 |
23534 |
23534 |
TNPO3 |
M-019949-00 |
1.1653026437585 |
none |
|
no |
|
Homologous recombination DNA double-strand break repair (HR-DSBR) (1) |
A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. |
Adamson et al. |
2012 |
22344029 |
Cell line |
DR-U2OS |
(HR-DSBR) DR-GFP reporter and DNA content |
Fluorescence |
Human siGENOME siRNA (G-005000-05) |
Genome-wide |
siRNA |
Relative HR ratio |
< ~0.4 OR > 1.88 |
Cutoff values correspond 2 standard deviations from the screen-wide mean |
GR00240-S-1 |
23534 |
NM_012470 |
TNPO3 |
M-019949-00 |
0.02 |
none |
|
yes |
|
TRAIL-induced apoptosis (1) |
A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. |
Kranz and Boutros |
2014 |
24442637 |
Cell line |
U251MG |
Viability |
Luminescence |
SMART-pool siRNA |
Genome-wide |
siRNA |
Z-score |
> 4 |
Author-submitted data |
GR00240-S-2 |
23534 |
NM_012470 |
TNPO3 |
M-019949-00 |
-0.81 |
none |
|
no |
Z-score -0.727 |
TRAIL-induced apoptosis (2) |
A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. |
Kranz and Boutros |
2014 |
24442637 |
Cell line |
U251MG |
Viability (synthetic lethal) |
Luminescence |
SMART-pool siRNA |
Genome-wide |
siRNA |
Differential score |
> 3.6 AND viability Z-score < 4 |
Author-submitted data. Z-scores from viability screen (1) are considered in score interpretation for this screen. |
GR00242-A-1 |
23534 |
NM_012470 |
TNPO3 |
np |
sp |
none |
|
no |
|
Selective autophagy regulation (1) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Sindbis virus (SIN) capsid SIN-mCherry.capsid and autophagosome GFP–LC3 protein expression |
Fluorescence |
siGenome |
Genome-wide |
siRNA |
Z-score |
Complex criteria |
|
GR00249-S |
23534 |
23534 |
TNPO3 |
J-019949-09 |
0.43125 |
none |
|
no |
number of cells compared to control (%): 83.52 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23534 |
23534 |
TNPO3 |
J-019949-09 |
0.03188 |
none |
|
no |
number of cells compared to control (%): 88.41 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23534 |
23534 |
TNPO3 |
M-019949-01 |
-0.04393 |
none |
|
no |
number of cells compared to control (%): 82.21 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23534 |
23534 |
TNPO3 |
s24030 |
-1.86135 |
Decreased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 95.34 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23534 |
23534 |
TNPO3 |
s24031 |
1.06432 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 73.69 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23534 |
23534 |
TNPO3 |
s24032 |
-0.38154 |
none |
|
no |
number of cells compared to control (%): 84.18 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00252-A-1 |
23534 |
23534 |
TNPO3 |
np |
-4.90495 |
Decreased viability after Maraba virus infection |
|
|
|
Oncolytic Maraba rhabdovirus infection (1) |
Virus-tumor interactome screen reveals ER stress response can reprogram resistant cancers for oncolytic virus-triggered caspase-2 cell death. |
Mahoney et al. |
2011 |
22014571 |
Cell line |
OVCAR-8 |
Viability |
Fluorescence |
np |
Genome-wide |
siRNA |
Composite MAD |
np |
All listed genes are final hits. Final hit if hit in > |
GR00252-A-2 |
23534 |
23534 |
TNPO3 |
np |
-4.06996 |
Decreased viability after Maraba virus infection |
|
|
|
Oncolytic Maraba rhabdovirus infection (2) |
Virus-tumor interactome screen reveals ER stress response can reprogram resistant cancers for oncolytic virus-triggered caspase-2 cell death. |
Mahoney et al. |
2011 |
22014571 |
Cell line |
U373 |
Viability |
Fluorescence |
np |
Genome-wide |
siRNA |
Composite MAD |
np |
All listed genes are final hits. Final hit if hit in > |
GR00252-A-3 |
23534 |
23534 |
TNPO3 |
np |
-3.75153 |
Decreased viability after Maraba virus infection |
|
|
|
Oncolytic Maraba rhabdovirus infection (3) |
Virus-tumor interactome screen reveals ER stress response can reprogram resistant cancers for oncolytic virus-triggered caspase-2 cell death. |
Mahoney et al. |
2011 |
22014571 |
Cell line |
NCI-H226 |
Viability |
Fluorescence |
np |
Genome-wide |
siRNA |
Composite MAD |
np |
All listed genes are final hits. Final hit if hit in > |
GR00253-A |
23534 |
NM_012470 |
TNPO3 |
np |
-1.478 |
Decreased hepcidin::fluc mRNA expression |
|
|
|
hepcidin regulation |
Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling. |
Mleczko-Sanecka et al. |
2014 |
24385536 |
Cell line |
Huh7 |
hepcidin::fluc mRNA expression |
Luminescence |
siGenome siARRAY SMARTpool |
Genome-wide |
siRNA |
Z-score |
> |
Cutoff < |
GR00255-A-1 |
23534 |
23534 |
TNPO3 |
TRCN0000038329, TRCN0000038330, TRCN0000038331, TRCN0000038332, TRCN0000038333 |
0.201035299 |
none |
|
|
|
Negative genetic interactions (1) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.0 |
HCT116 BLM-/- and HCT116 BLM+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-2 |
23534 |
23534 |
TNPO3 |
TRCN0000038329, TRCN0000038330, TRCN0000038331, TRCN0000038332, TRCN0000038333 |
0.203622392 |
none |
|
|
|
Negative genetic interactions (2) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.0 |
HCT116 MUS81-/- and HCT116 MUS81+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-3 |
23534 |
23534 |
TNPO3 |
TRCN0000038329, TRCN0000038330, TRCN0000038331, TRCN0000038332, TRCN0000038333 |
0.17694753 |
none |
|
|
|
Negative genetic interactions (3) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.2 |
HCT116 PTEN-/- and HCT116 PTEN+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-4 |
23534 |
23534 |
TNPO3 |
TRCN0000038329, TRCN0000038330, TRCN0000038331, TRCN0000038332, TRCN0000038333 |
0.18254529 |
none |
|
|
|
Negative genetic interactions (4) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.2 |
HCT116 PTTG1-/- and HCT116 PTTG1+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-5 |
23534 |
23534 |
TNPO3 |
TRCN0000038329, TRCN0000038330, TRCN0000038331, TRCN0000038332, TRCN0000038333 |
-0.086905808 |
none |
|
|
|
Negative genetic interactions (5) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -0.8 |
HCT116 KRASG13D/- and HCT116 KRAS+/- cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00300-A |
23534 |
|
TNPO3 |
TRCN0000038333, TRCN0000038332, TRCN0000038331, TRCN0000038330, TRCN0000038329 |
0 |
none |
|
|
|
Combinatorial effect with RAF inhibitor PLX4720 |
A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. |
Whittaker et al. |
2013 |
23288408 |
Cell line |
A375 |
shRNA abundance |
Sequencing |
TRC |
Genome-wide |
shRNA |
Number of shRNAs ranked Top1000 |
> 2 |
The A375 cell line used here harbours the BRAF V600E mutation and is therefore sensitive to RAF inhibitors. |
GR00303-A |
23534 |
NM_012470 |
TNPO3 |
np |
-2.06 |
none |
|
|
|
Clear cell renal cell carcinoma (ccRCC) survival regulation |
Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target |
Gerlinger et al. |
2012 |
22362593 |
Cell line |
VHL-deficient RCC4 |
Proliferation and Viability |
Fluorescence |
np |
Genome-wide |
siRNA |
Z-score |
< |
In the phenotype data duplicates were in the original document, which have been removed. |
GR00310-A-1 |
23534 |
23534 |
TNPO3 |
np |
0.38 |
none |
|
|
|
Sindbis virus (SINV) infection (1) |
Genome-Wide RNAi Screen Identifies Novel Host Proteins Required for Alphavirus Entry |
Ooi et al. |
2013 |
24367265 |
Cell line |
U2OS |
Sindbis virus (SINV) reporter |
Luminescence |
Ambion Silencer V3 |
Genome-wide |
siRNA |
Z-score |
< -3 OR > 2 |
|
|
23534 |
23534 |
TNPO3 |
np |
67.6 |
Inconclusive |
|
|
56,6% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
23534 |
NM_012470 |
TNPO3 |
np |
2.92 |
none |
|
|
|
TNF-alpha pathway regulation |
A Genome-Wide RNA Interference Screen Identifies Caspase 4 as a Factor Required for Tumor Necrosis Factor Alpha Signaling. |
Nickles et al. |
2012 |
22733992 |
Cell line |
HEK293T |
NFkappaB pathway reporter |
Luminescence |
Qiagen |
Genome-wide |
siRNA |
Z-score |
< |
Additional filters were a reduction in firefly luciferase levels by at least 50% compared to the mean of the experiment and a concomitant reduction of renilla luciferase expression of not more than 30%. |
GR00343-S |
23534 |
23534 |
TNPO3 |
TRCN0000038330 |
0.27249999999999996 |
none |
|
|
|
Lentiviral shRNA "Achilles Heel" screen |
Inhibition of the mitochondrial protease, ClpP, as a therapeutic strategy for human acute myeloid leukemia |
Cole et al. |
2015 |
26058080 |
Cell line |
K562 |
shRNA abundance |
Fluorescence |
Lentiviral shRNA library |
Genome-wide |
shRNA |
Log2 ratio |
< |
Comparison of day 21 vs. day 0 abundance data |
GR00343-S |
23534 |
23534 |
TNPO3 |
TRCN0000038329 |
0.9349999999999987 |
none |
|
|
|
Lentiviral shRNA "Achilles Heel" screen |
Inhibition of the mitochondrial protease, ClpP, as a therapeutic strategy for human acute myeloid leukemia |
Cole et al. |
2015 |
26058080 |
Cell line |
K562 |
shRNA abundance |
Fluorescence |
Lentiviral shRNA library |
Genome-wide |
shRNA |
Log2 ratio |
< |
Comparison of day 21 vs. day 0 abundance data |
GR00343-S |
23534 |
23534 |
TNPO3 |
TRCN0000038331 |
0.7349999999999994 |
none |
|
|
|
Lentiviral shRNA "Achilles Heel" screen |
Inhibition of the mitochondrial protease, ClpP, as a therapeutic strategy for human acute myeloid leukemia |
Cole et al. |
2015 |
26058080 |
Cell line |
K562 |
shRNA abundance |
Fluorescence |
Lentiviral shRNA library |
Genome-wide |
shRNA |
Log2 ratio |
< |
Comparison of day 21 vs. day 0 abundance data |
GR00343-S |
23534 |
23534 |
TNPO3 |
TRCN0000038333 |
1.0424999999999986 |
none |
|
|
|
Lentiviral shRNA "Achilles Heel" screen |
Inhibition of the mitochondrial protease, ClpP, as a therapeutic strategy for human acute myeloid leukemia |
Cole et al. |
2015 |
26058080 |
Cell line |
K562 |
shRNA abundance |
Fluorescence |
Lentiviral shRNA library |
Genome-wide |
shRNA |
Log2 ratio |
< |
Comparison of day 21 vs. day 0 abundance data |
GR00351-A-2 |
23534 |
23534 |
TNPO3 |
TRCN0000291605, TRCN0000307728, TRCN0000291604, TRCN0000038332, TRCN0000296949 |
sp |
Decreased vaccinia virus (VACV-LREV ) gene expression |
|
|
|
Orthopoxvirus infection (2) |
The Master Regulator of the Cellular Stress Response (HSF1) Is Critical for Orthopoxvirus Infection |
Filone et al. |
2014 |
24516381 |
Cell line |
A549 |
Vaccinia virus (VACV-LREV) gene expression |
Fluorescence |
TRC |
Selected genes |
shRNA |
Normalized RFU |
Complex criteria |
The vaccinia virus VACV-LREV expressed soluble Venus under an early promoter and soluble mCherry under a late promoter. |
|
23534 |
23534 |
TNPO3 |
|
-0.02 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00376-A-1 |
23534 |
23534 |
TNPO3 |
|
0.797635217 |
none |
|
|
|
Mitigators of SS1P-induced immunotoxicity |
Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity |
Pasetto et al. |
2015 |
25713356 |
Cell line |
KB cells |
Viability |
Luminescence |
Ambion Silencer Select Version 4 |
Genome-wide |
siRNA |
RSA P-value |
<0.001 |
SS1P was applied in a "high dose", ≈EC90, 13 ng/ml. Cutoff was derived from data submitted to Pubchem (ID 1117281). Reagent sequences but no ID |
GR00376-A-2 |
23534 |
23534 |
TNPO3 |
|
0.321278061 |
none |
|
|
|
Sensitizers of SS1P-induced immunotoxicity |
Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity |
Pasetto et al. |
2015 |
25713356 |
Cell line |
KB cells |
Viability |
Luminescence |
Ambion Silencer Select Version 4 |
Genome-wide |
siRNA |
RSA P-value |
<0.001 |
SS1P was applied in a "low dose", ≈EC30, 3 ng/ml. Cutoff was derived from data submitted to PubChem (ID 1117281). Reagent sequences but no ID |
|
23534 |
NM_012470 |
TNPO3 |
|
31.36 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00386-A-1 |
23534 |
23534 |
TNPO3 |
|
65.3712944607742 |
Decreased viability |
|
|
|
NOD2 stimulation by MDP |
A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. |
Warner et al. |
2014 |
25170077 |
Cell line |
HEK293 stably expressing NOD2 |
Viability |
Luminescence |
Dharmacon |
Genome-wide |
siRNA |
Percentage growth |
Decreased: <70, increased: >120 |
Reagent IDs not provided |
GR00386-A-2 |
23534 |
23534 |
TNPO3 |
|
5.1 |
none |
|
|
|
MDP-induced IL-8 secretion |
A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. |
Warner et al. |
2014 |
25170077 |
Cell line |
HEK293 stably expressing NOD2 |
IL-8 secretion |
ELISA |
Dharmacon |
Genome-wide |
siRNA |
Percent inhibition of IL-8 secretion |
Increased: <-300, Decreased: >60 |
Concentration of IL-8 was measured from cell supernatants by sandwich ELISA. IL-8 values (pg/ml) were normalized to IL-8 secreted in cells treated with RIPK2-specific siRNA (100% inhibition) and non-targeting siRNA (0% inhibition). Secondary validating screen assessed 554 genes whose silencing affected MDP-induced IL-8 secretion in the primary screen. Final validated IL-8 regulators (positive or negative) are listed in the comments column. Reagent IDs not provided |