| GR00016-A |
4358 |
4358 |
MPV17 |
np |
1.87 |
none |
|
no |
|
Wnt/beta-catenin pathway regulation |
Bruton's tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling. |
James et al. |
2009 |
19471023 |
Cell line |
RKO |
Wnt/beta-catenin pathway reporter |
Luminescence |
rp |
Selected genes |
siRNA |
Z-score |
> 2 |
|
GR00053-A |
4358 |
NM_002437 |
MPV17 |
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 |
4358 |
NM_002437 |
MPV17 |
np |
0.691 |
Decreased viability with paclitaxel |
|
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 |
4358 |
NM_002437 |
MPV17 |
np |
0.862 |
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 |
4358 |
NM_002437 |
MPV17 |
M-017720-00 |
0.11 |
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 |
4358 |
NM_002437 |
MPV17 |
M-017720-00 |
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 |
4358 |
ENSG00000115204 |
MPV17 |
ENSG00000115204 |
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 |
|
GR00151-A-1 |
4358 |
ENSG00000115204 |
MPV17 |
np |
0.245 |
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 |
4358 |
4358 |
MPV17 |
PL-50048 |
0.917 |
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 |
4358 |
NM_002437 |
MPV17 |
M-017720-00 |
-0.528939297532277 |
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 |
4358 |
ENSG00000115204 |
|
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 |
4358 |
4358 |
MPV17 |
M-017720-00 |
-0.662449391 |
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 |
GR00236-A-1 |
4358 |
4358 |
MPV17 |
M-017720-00 |
1.4068316211205 |
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 |
4358 |
NM_002437 |
MPV17 |
M-017720-00 |
1.54 |
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 |
4358 |
NM_002437 |
MPV17 |
M-017720-00 |
3.72 |
Decreased viability with TRAIL |
|
no |
Z-score 4.141 |
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 |
4358 |
NM_002437 |
MPV17 |
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 |
|
GR00247-A-1 |
4358 |
|
MPV17 |
np |
sp |
FOXO1 nuclear localization |
|
|
rank: 339 |
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 |
|
GR00247-A-2 |
4358 |
4358 |
MPV17 |
D-017720-01 |
sp |
none |
|
|
0/4 siRNAs validated |
Regulation of FOXO1 nuclear localization (2) |
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 |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
Reconfirmed gene if > |
GR00247-A-2 |
4358 |
4358 |
MPV17 |
D-017720-02 |
sp |
none |
|
|
0/4 siRNAs validated |
Regulation of FOXO1 nuclear localization (2) |
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 |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
Reconfirmed gene if > |
GR00247-A-2 |
4358 |
4358 |
MPV17 |
D-017720-03 |
sp |
none |
|
|
0/4 siRNAs validated |
Regulation of FOXO1 nuclear localization (2) |
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 |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
Reconfirmed gene if > |
GR00247-A-2 |
4358 |
4358 |
MPV17 |
D-017720-04 |
sp |
none |
|
|
0/4 siRNAs validated |
Regulation of FOXO1 nuclear localization (2) |
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 |
np |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
Reconfirmed gene if > |
GR00249-S |
4358 |
4358 |
MPV17 |
J-017720-09 |
1.13807 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 96.56 |
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 |
4358 |
4358 |
MPV17 |
M-017720-01 |
0.25041 |
none |
|
no |
number of cells compared to control (%): 73.64 |
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 |
4358 |
4358 |
MPV17 |
s226594 |
0.11405 |
none |
|
no |
number of cells compared to control (%): 95.06 |
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 |
4358 |
4358 |
MPV17 |
s8950 |
0.58734 |
none |
|
no |
number of cells compared to control (%): 89.39 |
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 |
4358 |
4358 |
MPV17 |
s8951 |
-0.01597 |
none |
|
no |
number of cells compared to control (%): 86.06 |
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 %. |
GR00253-A |
4358 |
NM_002437 |
MPV17 |
np |
1.014 |
none |
|
|
|
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 |
4358 |
4358 |
MPV17 |
TRCN0000127649, TRCN0000128669, TRCN0000129921, TRCN0000131038, TRCN0000131201 |
-0.325814113 |
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 |
4358 |
219770 |
GJD4 |
TRCN0000074123, TRCN0000074124, TRCN0000074125, TRCN0000074126, TRCN0000074127 |
0.021551582 |
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 |
4358 |
4358 |
MPV17 |
TRCN0000127649, TRCN0000128669, TRCN0000129921, TRCN0000131038, TRCN0000131201 |
0.784886218 |
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 |
4358 |
219770 |
GJD4 |
TRCN0000074123, TRCN0000074124, TRCN0000074125, TRCN0000074126, TRCN0000074127 |
0.137028372 |
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 |
4358 |
219770 |
GJD4 |
TRCN0000074123, TRCN0000074124, TRCN0000074125, TRCN0000074126, TRCN0000074127 |
0.247734412 |
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 |
4358 |
4358 |
MPV17 |
TRCN0000127649, TRCN0000128669, TRCN0000129921, TRCN0000131038, TRCN0000131201 |
0.543201349 |
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 |
4358 |
4358 |
MPV17 |
TRCN0000127649, TRCN0000128669, TRCN0000129921, TRCN0000131038, TRCN0000131201 |
0.855912687 |
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 |
4358 |
219770 |
GJD4 |
TRCN0000074123, TRCN0000074124, TRCN0000074125, TRCN0000074126, TRCN0000074127 |
0.490142073 |
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 |
4358 |
4358 |
MPV17 |
TRCN0000127649, TRCN0000128669, TRCN0000129921, TRCN0000131038, TRCN0000131201 |
-0.66076974 |
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) |
GR00255-A-5 |
4358 |
219770 |
GJD4 |
TRCN0000074123, TRCN0000074124, TRCN0000074125, TRCN0000074126, TRCN0000074127 |
-0.346462131 |
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) |
GR00257-A-1 |
4358 |
|
mpv17 |
11504 |
sp |
Large nuclei |
|
|
|
Cell division, migration and survival (1) |
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. |
Neumann et al. |
2010 |
20360735 |
Cell line |
HeLa |
H2B-GFP protein expression |
Fluorescence |
Mapped using ENSEMBL genome database version 27 |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
HeLa-H2B-GFP cells used. |
GR00293-A |
4358 |
|
MPV17 |
np |
-0.981 |
none |
|
|
|
Combinatorial effect with paclitaxel |
Mechanisms Promoting Escape from Mitotic Stress−Induced Tumor Cell Death |
Sinnott et al. |
2014 |
24860162 |
Cell line |
HCC366 |
Viability |
Luminescence |
Thermo-Fisher |
Genome-wide |
siRNA |
Z-score |
< -2.5 |
Final hits according to the author are indicated in the comment. |
GR00300-A |
4358 |
|
MPV17 |
TRCN0000131201, TRCN0000131038, TRCN0000127649, TRCN0000128669, TRCN0000129921 |
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 |
4358 |
NM_002437 |
MPV17 |
np |
0.56 |
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 |
4358 |
4358 |
MPV17 |
np |
-2.6 |
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 |
|
|
4358 |
4358 |
MPV17 |
np |
34 |
none |
|
|
67,9% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
4358 |
NM_002437 |
MPV17 |
np |
-0.3 |
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%. |
GR00327-A |
4358 |
4358 |
SUCLG1 |
CLL-H-024867 |
3.969226528998261 |
Increased shRNA abundance |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
4358 |
4358 |
SUCLG1 |
CLL-H-024868 |
0.31368766970775724 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
4358 |
4358 |
SUCLG1 |
CLL-H-024869 |
-1.8189201830117698 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
4358 |
4358 |
SUCLG1 |
CLL-H-024865 |
0.9203894289166802 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
4358 |
4358 |
SUCLG1 |
CLL-H-024866 |
-0.22989059719029448 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00360-A-1 |
4358 |
ENSG00000115204 |
MPV17 |
11504 |
0.9096000000000001 |
Mildly decreased CFP-tsO45G cell surface transport |
|
|
|
Secretory transport (1) |
Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway |
Simpson et al. |
2012 |
22660414 |
Cell line |
HeLa Kyoto |
CFP-tsO45G cell surface transport |
Fluorescence |
Ambion |
Genome-wide |
siRNA |
Deviation score |
< - 1 OR > 0.75 (mild: 0.75 - 1.0; strong: > 1.0) |
For validation screen see Secretory transport (2). |
GR00360-A-1 |
4358 |
ENSG00000115204 |
MPV17 |
11415 |
1.2668 |
Strongly decreased CFP-tsO45G cell surface transport |
|
|
|
Secretory transport (1) |
Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway |
Simpson et al. |
2012 |
22660414 |
Cell line |
HeLa Kyoto |
CFP-tsO45G cell surface transport |
Fluorescence |
Ambion |
Genome-wide |
siRNA |
Deviation score |
< - 1 OR > 0.75 (mild: 0.75 - 1.0; strong: > 1.0) |
For validation screen see Secretory transport (2). |
GR00360-A-2 |
4358 |
ENSG00000115204 |
MPV17 |
SI00647857 |
3.6995 |
Strongly decreased CFP-tsO45G cell surface transport |
|
|
|
Secretory transport (2) |
Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway |
Simpson et al. |
2012 |
22660414 |
Cell line |
HeLa Kyoto |
CFP-tsO45G cell surface transport |
Fluorescence |
Ambion and Qiagen |
Selected genes |
siRNA |
Deviation score |
> 1.0 |
For primary screen see Secretory transport (1). Several genes scored as hit but were not expressed in HeLa Kyoto cells, see comment. Qiagen custom: Reagent Sequences provided by authors. |
GR00363-A |
4358 |
4358 |
MPV17 |
11415, 11504, SI00647857, SI00647864, SI00647850, esi4285, SI00647843 |
sp |
Decreased endosome-nucleus distance (endosomes clustered in the perinuclear region) |
|
|
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. |
|
4358 |
4358 |
MPV17 |
|
-0.03999999999999998 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00376-A-1 |
4358 |
4358 |
MPV17 |
|
0.039226067 |
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 |
4358 |
4358 |
MPV17 |
|
0.337054603 |
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 |
GR00378-A |
4358 |
|
MPV17 |
|
0.897626677 |
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 |
|
4358 |
NM_002437 |
MPV17 |
|
31.735 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00386-A-1 |
4358 |
4358 |
MPV17 |
|
65.8494798700947 |
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 |
4358 |
4358 |
MPV17 |
|
-81.4 |
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 |