| GR00053-A |
1292 |
NM_001849 |
COL6A2 |
np |
sp |
none |
|
no |
|
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 |
1292 |
NM_001849 |
COL6A2 |
np |
0.825 |
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 |
1292 |
NM_001849 |
COL6A2 |
np |
1.109 |
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 |
1292 |
NM_001849 |
COL6A2 |
M-011621-00 |
1.08 |
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 |
1292 |
NM_001849 |
COL6A2 |
M-011621-00 |
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). |
GR00095-A |
1292 |
NM_001849 |
COL6A2 |
np |
np |
none |
|
|
|
p53 pathway components |
A large-scale RNAi screen in human cells identifies new components of the p53 pathway |
Berns et al. |
2004 |
15042092 |
Cell line |
BJ-TERT-tsLT fibroblasts |
Proliferation |
Colony-forming cell assay |
Nki library |
Genome-wide |
shRNA |
np |
np |
|
GR00098-A-1 |
1292 |
ENSG00000142173 |
COL6A2 |
ENSG00000142173 |
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 |
|
GR00123-A |
1292 |
NM_001849 |
COL6A2 |
147182, 147181, 147183 |
np |
none |
|
|
|
Combinatorial effect with nutlin-3 |
An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors |
Brummelkamp et al. |
2006 |
16474381 |
Cell line |
MCF-7 |
Viability |
Fluoresence |
Nki library |
Genome-wide |
shRNA |
log2 ratio |
np |
|
GR00151-A-1 |
1292 |
ENSG00000142173 |
COL6A2 |
np |
-0.942 |
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 |
1292 |
1292 |
COL6A2 |
PL-50019 |
0.796 |
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 |
1292 |
NM_001849 |
COL6A2 |
M-011621-00 |
-1.86782007673582 |
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 |
1292 |
ENSG00000142173 |
|
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 |
1292 |
1292 |
COL6A2 |
M-011621-00 |
-0.620266239 |
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 |
GR00207-A-1 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with paclitaxel (1) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-8 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-10 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with carboplatin (4) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-5 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-11 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
decreased viability with 1.5 IC50 carboplatin |
Combinatorial effect with carboplatin (5) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
IGROV-1 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-12 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
no |
decreased viability with 0.75 IC50 carboplatin |
Combinatorial effect with carboplatin (6) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-4 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-2 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
decreased viability with 1.5 IC50 paclitaxel |
Combinatorial effect with paclitaxel (2) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
Sk-Ov-3 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-3 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with paclitaxel (3) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-3 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-4 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with paclitaxel (4) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-5 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-5 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with paclitaxel (5) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
IGROV-1 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-6 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
no |
|
Combinatorial effect with paclitaxel (6) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-4 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-7 |
1292 |
|
COL6A2 |
np |
1.26 |
none |
|
yes |
|
Combinatorial effect with carboplatin (1) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-8 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 |
|
GR00207-A-8 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with carboplatin (2) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
Sk-Ov-3 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00207-A-9 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
yes |
|
Combinatorial effect with carboplatin (3) |
Autotaxin delays apoptosis induced by carboplatin in ovarian cancer cells. |
Vidot et al. |
2010 |
20100569 |
Cell line |
OVCAR-3 |
Viability (synthetic lethal) |
Colorimetrics |
np |
Selected genes |
siRNA |
Sensitization index |
< 0.75 for both 0.75 and 1.50 IC50 |
|
GR00236-A-1 |
1292 |
1292 |
COL6A2 |
M-011621-00 |
1.86298981852284 |
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 |
1292 |
NM_001849 |
COL6A2 |
M-011621-00 |
0.3 |
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 |
1292 |
NM_001849 |
COL6A2 |
M-011621-00 |
0.14 |
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. |
GR00242-A-1 |
1292 |
NM_001849 |
COL6A2 |
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 |
1292 |
|
COL6A2 |
np |
sp |
none |
|
|
rank: 9200 |
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 |
1292 |
1292 |
COL6A2 |
J-011621-05 |
-0.86139 |
none |
|
no |
number of cells compared to control (%): 77.71 |
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 |
1292 |
1292 |
COL6A2 |
M-011621-01 |
-2.82599 |
Decreased viability |
|
no |
number of cells compared to control (%): 6.42 |
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 |
1292 |
1292 |
COL6A2 |
s3314 |
-0.63923 |
none |
|
no |
number of cells compared to control (%): 98.47 |
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 |
1292 |
1292 |
COL6A2 |
s3315 |
-1.95811 |
Decreased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 71.53 |
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 %. |
GR00249-S |
1292 |
1292 |
COL6A2 |
s3316 |
2.63279 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 91.74 |
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 |
1292 |
1292 |
COL6A2 |
np |
np |
none |
|
|
|
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 |
1292 |
1292 |
COL6A2 |
np |
-3.65746 |
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 |
1292 |
1292 |
COL6A2 |
np |
-2.00627 |
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 |
1292 |
NM_001849 |
COL6A2 |
np |
-0.087 |
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 |
1292 |
1292 |
COL6A2 |
TRCN0000116847, TRCN0000116848, TRCN0000116849, TRCN0000116850, TRCN0000116851 |
-0.03789884 |
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 |
1292 |
1292 |
COL6A2 |
TRCN0000116847, TRCN0000116848, TRCN0000116849, TRCN0000116850, TRCN0000116851 |
0.290353809 |
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 |
1292 |
1292 |
COL6A2 |
TRCN0000116847, TRCN0000116848, TRCN0000116849, TRCN0000116850, TRCN0000116851 |
-1.740893658 |
Negative genetic interaction between PTEN-/- and PTEN+/+ |
|
|
|
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 |
1292 |
1292 |
COL6A2 |
TRCN0000116847, TRCN0000116848, TRCN0000116849, TRCN0000116850, TRCN0000116851 |
0.519317483 |
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 |
1292 |
1292 |
COL6A2 |
TRCN0000116847, TRCN0000116848, TRCN0000116849, TRCN0000116850, TRCN0000116851 |
0.733016775 |
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) |
GR00293-A |
1292 |
|
COL6A2 |
np |
-0.57 |
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 |
1292 |
|
COL6A2 |
TRCN0000116848, TRCN0000116847, TRCN0000116849, TRCN0000116851, TRCN0000116850 |
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 |
1292 |
NM_001849 |
COL6A2 |
np |
0.65 |
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 |
1292 |
1292 |
COL6A2 |
np |
1.5 |
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 |
|
|
1292 |
1292 |
COL6A2 |
np |
45.9 |
none |
|
|
84,5% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
1292 |
NM_001849 |
COL6A2 |
np |
-0.61 |
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 |
1292 |
1292 |
COL6A2 |
np |
1.126 |
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). |
GR00327-A |
1292 |
1292 |
TSPAN7 |
CLL-H-026272 |
-0.8322693464209888 |
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 |
1292 |
1292 |
TSPAN7 |
CLL-H-026275 |
0.6099704494044186 |
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 |
1292 |
1292 |
TSPAN7 |
CLL-H-026273 |
-1.2601031216782899 |
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 |
1292 |
4546 |
COL6A2 |
CLL-H-006548 |
0.9742457028388463 |
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 |
1292 |
4546 |
COL6A2 |
CLL-H-006547 |
-0.4788183986678473 |
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 |
1292 |
1292 |
TSPAN7 |
CLL-H-026274 |
0.29561281969364867 |
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 |
1292 |
4546 |
COL6A2 |
CLL-H-006546 |
-0.720576736042533 |
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 |
1292 |
4546 |
COL6A2 |
CLL-H-006549 |
-0.2264461705546982 |
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 |
1292 |
1292 |
TSPAN7 |
CLL-H-026271 |
0.41647132499751 |
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 |
1292 |
4546 |
COL6A2 |
CLL-H-006550 |
0.8545318762530602 |
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 |
1292 |
1292 |
TSPAN7 |
CLL-H-026270 |
0.015007464298722274 |
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 |
1292 |
ENSG00000142173 |
COL6A2 |
10540 |
0.8922666666666671 |
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). |
|
1292 |
1292 |
COL6A2 |
|
0.05 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00376-A-1 |
1292 |
1292 |
COL6A2 |
|
0.355688992 |
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 |
1292 |
1292 |
COL6A2 |
|
0.053226153 |
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 |
1292 |
|
COL6A2 |
|
-0.735320242 |
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 |
|
1292 |
NM_001849 |
COL6A2 |
|
14.827 |
Decreased viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00381-A-2 |
1292 |
|
COL6A2 |
|
28.766484614359932 |
none |
|
|
Extracellular Space; other |
Regulation of mammary epithelial cell growth (2) |
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. |
Burleigh et al. |
2015 |
25572802 |
Cell line |
184-hTERT-L9 (mammary epithelial cells) |
Viability |
Count |
Dharmacon siGENOME |
Selected genes |
siRNA |
Percent growth |
< 25 % AND p-value < 0.05 |
388 genes from screen (1) showing <25% growth and suspected or confirmed to be present in transmembrane or extracellular space, and secreted proteins were selected for this secondary screening. Not all of the final hits are represented since more data was taken into account for the final selection. For reagents information check screen (1) |
GR00381-A-3 |
1292 |
|
COL6A2 |
|
23.860837438423648 |
Decreased viability |
|
|
Extracellular Space; other |
Regulation of mammary epithelial cell growth (3) |
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. |
Burleigh et al. |
2015 |
25572802 |
Cell line |
184-hTERT-E11 (mammary epithelial cells) |
Viability |
Count |
Dharmacon siGENOME |
Selected genes |
siRNA |
Percent growth |
< 25 % AND p-value < 0.05 |
184-hTERT-E11 differs from 184-hTERT-L9 only in the position of hTERT insertion. 388 genes from screen (1) showing <25% growth and suspected or confirmed to be present in transmembrane or extracellular space, and secreted proteins were selected for this secondary screening. Not all of the final hits are represented since more data was taken into account for the final selection. For reagents information check screen (1) |
GR00386-A-1 |
1292 |
1292 |
COL6A2 |
|
90.5606844186725 |
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 |
1292 |
1292 |
COL6A2 |
|
-6.1 |
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 |