| GR00057-A-1 |
114971 |
XM_374879 |
LOC114971 |
M-029988-00 |
-0.32 |
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-1 |
114971 |
NM_016506 |
KBTBD4 |
M-018888-00 |
1.49 |
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 |
114971 |
XM_374879 |
LOC114971 |
M-029988-00 |
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). |
GR00057-A-2 |
114971 |
NM_016506 |
KBTBD4 |
M-018888-00 |
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). |
GR00133-A-1 |
114971 |
114971 |
PLIP |
np |
0.124309 |
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 |
114971 |
114971 |
PTPMT1 |
263800 |
19.91 |
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 |
114971 |
114971 |
PTPMT1 |
263800 |
-9.48 |
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 |
114971 |
114971 |
PTPMT1 |
263801 |
-50.39 |
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 |
|
GR00149-A-1 |
114971 |
114971 |
PTPMT1 |
263801 |
85.16 |
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 |
114971 |
114971 |
PTPMT1 |
263802 |
-68.71 |
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 |
114971 |
114971 |
PTPMT1 |
263802 |
-32.21 |
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 |
114971 |
114971 |
PTPMT1 |
272744 |
-20.43 |
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 |
114971 |
114971 |
PTPMT1 |
272744 |
-18.93 |
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 |
114971 |
ENSG00000110536 |
PTPMT1 |
np |
0.209 |
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 |
|
GR00180-A-1 |
114971 |
114971 |
PTPMT1 |
PL-50015 |
0.836 |
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 |
114971 |
NM_016506 |
KBTBD4 |
M-018888-00 |
-0.426528349206532 |
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 |
|
GR00184-A-1 |
114971 |
XM_374879 |
PTPMT1 |
M-029988-00 |
-0.765558190873976 |
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 |
114971 |
ENSG00000110536 |
PTPMT1 |
PTPMT1 esi_L, PTPMT1 esi_R |
sp |
none |
|
yes |
|
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 |
|
GR00196-A-2 |
114971 |
ENSG00000110536 |
PTPMT1 |
PTPMT1 esi_L1, PTPMT1 esi_R1, PTPMT1 esi_L2, PTPMT1 esi_R2 |
sp |
Decreased TP53 protein expression ratio (wild-type / TP53 knockout cells) |
|
no |
|
TP53 interactions (2) |
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 |
Fluorescence |
Custom-made |
Selected genes |
esiRNA |
Z-score |
np |
|
GR00197-A-1 |
114971 |
114971 |
PTPMT1 |
M-029988-00 |
-1.033252529 |
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 |
GR00197-A-1 |
114971 |
55709 |
KBTBD4 |
M-018888-00 |
0.08959247 |
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 |
GR00204-A-1 |
114971 |
BC020242 |
PTPMT1 |
np |
17.126 |
none |
|
yes |
pooled siRNAs |
RTK/Ras pathway regulation (1) |
Phosphatome profiling reveals PTPN2, PTPRJ and PTEN as potent negative regulators of PKB/Akt activation in Ras-mutated cancer cells. |
Omerovic et al. |
2010 |
19922411 |
Cell line |
A549 |
Erk phosphorylation |
Fluorescence |
np |
Phosphatases |
siRNA |
Percentage |
Top 20 |
Additional information about a secondary screen (Panc-08-13 cells) |
GR00204-A-2 |
114971 |
BC020242 |
PTPMT1 |
np |
32.838 |
none |
|
no |
pooled siRNAs |
RTK/Ras pathway regulation (2) |
Phosphatome profiling reveals PTPN2, PTPRJ and PTEN as potent negative regulators of PKB/Akt activation in Ras-mutated cancer cells. |
Omerovic et al. |
2010 |
19922411 |
Cell line |
A549 |
Akt phosphorylation |
Fluorescence |
np |
Phosphatases |
siRNA |
Percentage |
Top 20 |
Additional information about a secondary screen (Panc-08-13 cells) |
GR00205-A |
114971 |
114971 |
PTPMT1 |
SI00687183, SI00687190, SI00687197 |
np |
none |
|
no |
|
Mitotic exit regulation |
Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. |
Schmitz et al. |
2010 |
20711181 |
Cell line |
HeLa |
H2B and IBB protein expression |
Fluorescence |
Human siRNA phosphatase V3.0 library |
Phosphatases |
siRNA |
Z-score |
> 3 |
Author-reviewed data. HeLa Kyoto strain |
GR00221-A-1 |
114971 |
|
PLIP |
TRCN0000052685 |
-2.23 |
Decreased viability |
|
yes |
essential gene |
Proliferation of cells with active beta-catenin (1) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MCF-7 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-1 |
114971 |
|
PLIP |
TRCN0000052684 |
-1.01 |
Decreased viability |
|
yes |
essential gene |
Proliferation of cells with active beta-catenin (1) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MCF-7 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-1 |
114971 |
|
PLIP |
TRCN0000052687 |
2.09 |
none |
|
yes |
essential gene |
Proliferation of cells with active beta-catenin (1) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MCF-7 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-2 |
114971 |
|
PLIP |
TRCN0000052685 |
-1.36 |
Decreased viability |
|
yes |
|
Proliferation of cells with active beta-catenin (2) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-231 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-2 |
114971 |
|
PLIP |
TRCN0000052684 |
0.4 |
none |
|
yes |
|
Proliferation of cells with active beta-catenin (2) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-231 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-2 |
114971 |
|
PLIP |
TRCN0000052687 |
0.89 |
none |
|
yes |
|
Proliferation of cells with active beta-catenin (2) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-231 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-3 |
114971 |
|
PLIP |
TRCN0000052685 |
-2 |
Decreased viability |
|
yes |
|
Proliferation of cells with active beta-catenin (3) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-453 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-3 |
114971 |
|
PLIP |
TRCN0000052687 |
-0.72 |
none |
|
yes |
|
Proliferation of cells with active beta-catenin (3) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-453 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
GR00221-A-3 |
114971 |
|
PLIP |
TRCN0000052684 |
-0.28 |
none |
|
yes |
|
Proliferation of cells with active beta-catenin (3) |
CK1epsilon is required for breast cancers dependent on beta-catenin activity. |
Kim et al. |
2010 |
20126544 |
Cell line |
MDA-MB-453 |
Viability |
Luminescence |
TRC shRNA Library |
Kinases |
shRNA |
B-score |
< -1 |
Essential gene: gene with B-score < -1 for > |
|
114971 |
XM_374879 |
PTPMT1 |
np |
1.505086 |
none |
|
no |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00236-A-1 |
114971 |
114971 |
PTPMT1 |
M-029988-00 |
1.67773899005399 |
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 |
GR00236-A-1 |
114971 |
55709 |
KBTBD4 |
M-018888-00 |
0.454896918813105 |
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 |
114971 |
XM_374879 |
LOC114971 |
M-029988-00 |
-0.11 |
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-1 |
114971 |
NM_016506 |
KBTBD4 |
M-018888-00 |
-0.01 |
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 |
114971 |
XM_374879 |
LOC114971 |
M-029988-00 |
-0.43 |
none |
|
no |
Z-score -0.5395 |
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. |
GR00240-S-2 |
114971 |
NM_016506 |
KBTBD4 |
M-018888-00 |
-0.67 |
none |
|
no |
Z-score -0.659 |
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. |
GR00247-A-1 |
114971 |
|
PTPMT1 |
np |
sp |
none |
|
|
rank: 10763 |
Regulation of FOXO1 nuclear localization (1) |
Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. |
Senapedis et al. |
2011 |
21460183 |
Cell line |
U2OS |
EGFP-FOXO1a protein expression and DNA content |
Fluorescence |
Human Genome library |
Genome-wide |
siRNA |
Complex, sp |
Complex criteria |
|
GR00249-S |
114971 |
114971 |
PTPMT1 |
J-029988-05 |
1.52293 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 64.04 |
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 |
114971 |
114971 |
PTPMT1 |
M-029988-02 |
-0.09928 |
none |
|
no |
number of cells compared to control (%): 59.86 |
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 |
114971 |
55709 |
KBTBD4 |
s31309 |
1.56324 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 96.53 |
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 %. |
GR00250-A-1 |
114971 |
55709 |
KBTBD4 |
M-018888-00 |
sp |
none |
|
|
duplicate screen |
Combinatorial effect with MLN4924, a NAE inhibitor (1) |
Novel DNA damage checkpoints mediating cell death induced by the NEDD8-activating enzyme inhibitor MLN4924. |
Blank et al. |
2013 |
23100467 |
Cell line |
A375 |
Viability (synthetic lethal) |
Luminescence |
np |
Genome-wide |
siRNA |
Complex, sp |
Complex criteria |
Phenotypes for 650 nmol/L MLN4924. Additional information about screens with 250 nmol/L MLN4924. |
GR00250-A-2 |
114971 |
55709 |
KBTBD4 |
D-018888-02 |
sp |
Synthetic lethal with MLN4924 (a NAE inhibitor) |
|
|
sextuplicate screen |
Combinatorial effect with MLN4924, a NAE inhibitor (2) |
Novel DNA damage checkpoints mediating cell death induced by the NEDD8-activating enzyme inhibitor MLN4924. |
Blank et al. |
2013 |
23100467 |
Cell line |
A375 |
Viability (synthetic lethal) |
Luminescence |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
Phenotypes for 650 nmol/L MLN4924. Additional information about screens with 250 nmol/L MLN4924. |
GR00255-A-1 |
114971 |
55709 |
KBTBD4 |
TRCN0000139228, TRCN0000140781, TRCN0000141375, TRCN0000144516, TRCN0000144852 |
0.147645342 |
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-1 |
114971 |
114971 |
PTPMT1 |
TRCN0000052684, TRCN0000052685, TRCN0000052687 |
-0.051762869 |
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 |
114971 |
114971 |
PTPMT1 |
TRCN0000052684, TRCN0000052685, TRCN0000052687 |
0.156596353 |
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-2 |
114971 |
55709 |
KBTBD4 |
TRCN0000139228, TRCN0000140781, TRCN0000141375, TRCN0000144516, TRCN0000144852 |
-0.341558629 |
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 |
114971 |
114971 |
PTPMT1 |
TRCN0000052684, TRCN0000052685, TRCN0000052687 |
0.202226142 |
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-3 |
114971 |
55709 |
KBTBD4 |
TRCN0000139228, TRCN0000140781, TRCN0000141375, TRCN0000144516, TRCN0000144852 |
0.543309419 |
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 |
114971 |
114971 |
PTPMT1 |
TRCN0000052684, TRCN0000052685, TRCN0000052687 |
0.652602549 |
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-4 |
114971 |
55709 |
KBTBD4 |
TRCN0000139228, TRCN0000140781, TRCN0000141375, TRCN0000144516, TRCN0000144852 |
-0.313669258 |
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 |
114971 |
55709 |
KBTBD4 |
TRCN0000139228, TRCN0000140781, TRCN0000141375, TRCN0000144516, TRCN0000144852 |
-1.132075846 |
Negative genetic interaction between KRASG13D/+ and KRAS+/- |
|
|
|
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) |
GR00255-A-5 |
114971 |
114971 |
PTPMT1 |
TRCN0000052684, TRCN0000052685, TRCN0000052687 |
0.393972551 |
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 |
114971 |
|
PTPMT1 |
TRCN0000052687, TRCN0000052684, TRCN0000052685 |
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. |
GR00300-A |
114971 |
|
KBTBD4 |
TRCN0000139228, TRCN0000144516, TRCN0000144852, TRCN0000141375, TRCN0000140781 |
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. |
GR00310-A-1 |
114971 |
|
PTPMT1 |
np |
-0.94 |
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 |
|
|
114971 |
114971 |
PTPMT1 |
np |
11.9 |
none |
|
|
80,3% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
114971 |
BC020242 |
PTPMT1 |
np |
-0.92 |
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%. |
GR00318-A |
114971 |
114971 |
LOC114971 |
np |
0.713 |
none |
|
|
siRNA set: druggable genome |
Huntingtin toxicity |
A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington’s Disease |
Miller et al. |
2012 |
23209424 |
Cell line |
HEK293T |
Caspase 3/7 activity |
Fluorescence |
Dharmacon |
Selected genes |
siRNA |
Sum of normalized caspase 3/7 activity mean and standard error |
< 0.683 |
HEK293T cells were cotransfected with mutant Huntingtin fused to GFP (Htt1-558141Q-GFP). |
GR00363-A |
114971 |
114971 |
PTPMT1 |
QiagenNoID_31, SI00687183, SI00687197, SI00687204 |
sp |
Increased transferrin (TF) endocytosis |
|
|
strong |
Endocytosis regulation |
Systems survey of endocytosis by multiparametric image analysis. |
Collinet et al. |
2010 |
20190736 |
Cell line |
HeLa |
Transferrin (TF) and epidermal growth factor (EGF) subcellular localisation, DNA content |
Fluorescence |
Ambion, Qiagen and esiRNA library (Kittler et al.) |
Genome-wide |
siRNA |
Complex, sp |
Complex criteria |
Two hit categories: "strong" (maximum of Prob Chi2, Prob Chi2 EGF, Prob Chi2 Tfn > 0.95) and "weak but specific" (maximum of Prob Chi2, Prob Chi2 EGF, Prob Chi2 Tfn < 0.95 but Phenoscore > 0.95). Additional information about secondary screens with kinase and phospatase libraries. |
|
114971 |
114971 |
PTPMT1 |
|
-0.009999999999999981 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00371-A-1 |
114971 |
114971 |
PTPMT1 |
|
-0.0983002333112 |
none |
|
|
Dharmacon |
Nanog expression in absence of bFGF and TGFbeta |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-2 |
114971 |
PTPMT1 |
114971 |
|
-0.870268315503 |
none |
|
|
Dharmacon |
Nanog expression in presence of TGFbeta inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-3 |
114971 |
114971 |
PTPMT1 |
|
0.526465952658 |
none |
|
|
Dharmacon |
Nanog expression in presence of MEK inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-4 |
114971 |
114971 |
PTPMT1 |
|
-0.53525709075 |
none |
|
|
Dharmacon |
Nanog expression in presence of PI3K inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-5 |
114971 |
114971 |
PTPMT1 |
|
-0.62787077368 |
none |
|
|
Dharmacon |
Nanog expression in presence of retinoic acid |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00378-A |
114971 |
|
PTPMT1 |
|
-0.319744131 |
none |
|
|
|
Poliovirus vaccine production |
Engineering Enhanced Vaccine Cell Lines To Eradicate Vaccine-Preventable Diseases: the Polio End Game |
van der Sanden et al. |
2015 |
26581994 |
Cell line |
HEp-2C |
Infection with Attenuated Poliovirus |
ELISA |
Dharmacon |
Genome-wide |
siRNA |
Z-score |
> |
For infection, a single lot of the attenuated Sabin type 2 poliovirus was used for the screen. Gene IDs were not provided, only the gene name/symbol |
GR00386-A-1 |
114971 |
114971 |
PTPMT1 |
|
86.7985377364547 |
none |
|
|
|
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 |
114971 |
114971 |
PTPMT1 |
|
-50.6 |
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 |