| GR00053-A |
51538 |
NM_016505 |
PS1D |
np |
sp |
Increased gamma-H2AX phosphorylation |
|
no |
group 2 |
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 |
51538 |
NM_016505 |
PS1D |
np |
1.001 |
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 |
51538 |
NM_016505 |
PS1D |
np |
0.858 |
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 |
51538 |
NM_016505 |
PS1D |
M-016869-00 |
-0.76 |
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 |
51538 |
NM_016505 |
PS1D |
M-016869-00 |
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 |
51538 |
ENSG00000121766 |
ZCCHC17 |
ENSG00000121766 |
sp |
Increased G1 DNA content |
|
yes |
did not validate with resynthesized esiRNA |
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 |
|
GR00098-A-3 |
51538 |
ENSG00000121766 |
ZCCHC17 |
ENSG00000121766 |
-1.2 |
none |
|
yes |
|
Cell division (3) |
Genome-scale RNAi profiling of cell division in human tissue culture cells. |
Kittler et al. |
2007 |
17994010 |
Cell line |
HeLa |
Histone H3 phosphorylation; alpha-tubulin and pericentrin protein expression |
Fluorescence |
rp |
Selected genes |
esiRNA |
Mitotic index |
> |
|
GR00098-A-4 |
51538 |
ENSG00000121766 |
ZCCHC17 |
ENSG00000121766 |
-1.5 |
none |
|
no |
|
Cell division (4) |
Genome-scale RNAi profiling of cell division in human tissue culture cells. |
Kittler et al. |
2007 |
17994010 |
Cell line |
HeLa |
Cell size (forward scatter) |
Flow cytometry |
rp |
Selected genes |
esiRNA |
Cell size |
> |
|
GR00151-A-1 |
51538 |
ENSG00000121766 |
ZCCHC17 |
np |
-0.414 |
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 |
51538 |
51538 |
ZCCHC17 |
PL-50058 |
0.434 |
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 |
51538 |
NM_016505 |
ZCCHC17 |
M-016869-00 |
-0.045694087697274 |
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 |
51538 |
ENSG00000121766 |
|
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 |
51538 |
51538 |
ZCCHC17 |
M-016869-00 |
-0.719494663 |
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 |
GR00226-A |
51538 |
51538 |
PS1D |
PS1D_siRNA_2 |
0.172118732843977 |
Decreased HIV-1 infection |
|
yes |
|
HIV-1 infection |
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. |
König et al. |
2008 |
18854154 |
Cell line |
293T |
VSV-G HIV-1 reporter and viability |
Luminescence |
np |
Genome-wide |
siRNA |
Median evidence score |
Complex criteria |
Additional information about MLV and AAV infection screens |
GR00226-A |
51538 |
51538 |
PS1D |
PS1D_siRNA_1 |
0.0814 |
Decreased HIV-1 infection |
|
yes |
|
HIV-1 infection |
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. |
König et al. |
2008 |
18854154 |
Cell line |
293T |
VSV-G HIV-1 reporter and viability |
Luminescence |
np |
Genome-wide |
siRNA |
Median evidence score |
Complex criteria |
Additional information about MLV and AAV infection screens |
GR00236-A-1 |
51538 |
51538 |
ZCCHC17 |
M-016869-00 |
1.09396809972191 |
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 |
51538 |
NM_016505 |
PS1D |
M-016869-00 |
-0.03 |
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 |
51538 |
NM_016505 |
PS1D |
M-016869-00 |
-0.77 |
none |
|
no |
Z-score -0.736 |
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 |
51538 |
NM_016505 |
PS1D |
np |
sp |
Decreased Sindbis virus (SIN) capsid and autophagosome LC3 protein colocalization |
|
yes |
2/4 siRNAs confirmed |
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 |
|
GR00242-A-2 |
51538 |
51538 |
ZCCHC17 |
D-016869-01 |
0.29 |
none |
|
yes |
|
Selective autophagy regulation (2) |
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 |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-2 |
51538 |
51538 |
ZCCHC17 |
D-016869-02 |
0.034 |
Decreased Sindbis virus (SIN) capsid and autophagosome LC3 protein colocalization |
|
yes |
|
Selective autophagy regulation (2) |
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 |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-2 |
51538 |
51538 |
ZCCHC17 |
D-016869-03 |
3.8e-23 |
Decreased Sindbis virus (SIN) capsid and autophagosome LC3 protein colocalization |
|
yes |
|
Selective autophagy regulation (2) |
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 |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-2 |
51538 |
51538 |
ZCCHC17 |
D-016869-04 |
0.49 |
none |
|
yes |
|
Selective autophagy regulation (2) |
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 |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-3 |
51538 |
51538 |
ZCCHC17 |
D-016869-01 |
0.015 |
Decreased viability after sindbis virus (SIN) dsTE12Q infection |
|
yes |
|
Selective autophagy regulation (3) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Viability |
Luminescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-3 |
51538 |
51538 |
ZCCHC17 |
D-016869-02 |
0.037 |
Decreased viability after sindbis virus (SIN) dsTE12Q infection |
|
yes |
|
Selective autophagy regulation (3) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Viability |
Luminescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-3 |
51538 |
51538 |
ZCCHC17 |
D-016869-03 |
0.03 |
Decreased viability after sindbis virus (SIN) dsTE12Q infection |
|
yes |
miRNA seeds (7-8mer): 1 |
Selective autophagy regulation (3) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Viability |
Luminescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-3 |
51538 |
51538 |
ZCCHC17 |
D-016869-04 |
0.2 |
none |
|
yes |
miRNA seeds (7-8mer): 4 |
Selective autophagy regulation (3) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Viability |
Luminescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-4 |
51538 |
55194 |
ZCCHC17 |
D-016869-01 |
3.8e-10 |
Decreased mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
|
no |
|
Selective autophagy regulation (4) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa |
Mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
Fluorescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-4 |
51538 |
55194 |
ZCCHC17 |
D-016869-02 |
4.4e-05 |
Decreased mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
|
no |
|
Selective autophagy regulation (4) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa |
Mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
Fluorescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-4 |
51538 |
2176 |
ZCCHC17 |
D-016869-03 |
1.1e-18 |
Decreased mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
|
no |
miRNA seeds (7-8mer): 1 |
Selective autophagy regulation (4) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa |
Mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
Fluorescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-4 |
51538 |
2188 |
ZCCHC17 |
D-016869-04 |
0.14 |
none |
|
no |
miRNA seeds (7-8mer): 4 |
Selective autophagy regulation (4) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa |
Mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
Fluorescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00242-A-4 |
51538 |
51538 |
DPF3 |
D-012798-19 |
0.00036 |
Decreased mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
|
no |
|
Selective autophagy regulation (4) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa |
Mitophagy mCherry-Parkin protein expression after carbonyl cyanide m-chlorphenylhydrazone (CCCP) stimulation |
Fluorescence |
np |
Selected genes |
siRNA |
p-value |
< 0.05 |
|
GR00247-A-1 |
51538 |
|
ZCCHC17 |
np |
sp |
none |
|
|
rank: 12329 |
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 |
51538 |
51538 |
PS1D |
J-016869-17 |
0.2486 |
none |
|
no |
number of cells compared to control (%): 79.56 |
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 |
51538 |
51538 |
PS1D |
M-016869-00 |
0.8183 |
none |
|
no |
number of cells compared to control (%): 73.20 |
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 |
51538 |
51538 |
ZCCHC17 |
s28291 |
0.07098 |
none |
|
no |
number of cells compared to control (%): 100.63 |
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 |
51538 |
51538 |
ZCCHC17 |
s28292 |
0.3191 |
none |
|
no |
number of cells compared to control (%): 85.40 |
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 |
51538 |
51538 |
ZCCHC17 |
s28293 |
0.87667 |
none |
|
no |
number of cells compared to control (%): 98.52 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00253-A |
51538 |
NM_016505 |
PS1D |
np |
-0.79 |
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 < |
GR00254-A |
51538 |
|
ZCCHC17 |
np |
np |
none |
|
|
|
SMN2 splicing regulation |
Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. |
Xiao et al. |
2012 |
22325991 |
Cell line |
HeLa |
SMN2-based splicing reporter expression |
Real-time PCR |
rp |
RNA-binding proteins |
esiRNA |
SMN2 FL/deltaexon 7 ratio |
np |
|
GR00255-A-1 |
51538 |
51538 |
ZCCHC17 |
TRCN0000062683, TRCN0000062685, TRCN0000062686, TRCN0000062687 |
-0.053852797 |
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 |
51538 |
51538 |
ZCCHC17 |
TRCN0000062683, TRCN0000062685, TRCN0000062686, TRCN0000062687 |
0.170091635 |
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 |
51538 |
51538 |
ZCCHC17 |
TRCN0000062683, TRCN0000062685, TRCN0000062686, TRCN0000062687 |
0.101064304 |
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 |
51538 |
51538 |
ZCCHC17 |
TRCN0000062683, TRCN0000062685, TRCN0000062686, TRCN0000062687 |
-0.339270766 |
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 |
51538 |
51538 |
ZCCHC17 |
TRCN0000062683, TRCN0000062685, TRCN0000062686, TRCN0000062687 |
-0.174413163 |
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 |
51538 |
|
PS1D |
np |
-1.078 |
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 |
51538 |
|
ZCCHC17 |
TRCN0000062683, TRCN0000062687, TRCN0000062686, TRCN0000062685 |
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 |
51538 |
NM_016505 |
PS1D |
np |
2.18 |
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 |
51538 |
51538 |
PS1D |
np |
0.89 |
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 |
|
|
51538 |
51538 |
ZCCHC17 |
np |
13.7 |
none |
|
|
101,2% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
51538 |
NM_016505 |
PS1D |
np |
3.11 |
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%. |
GR00360-A-1 |
51538 |
ENSG00000121766 |
ZCCHC17 |
122922 |
1.0456 |
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 |
51538 |
ENSG00000121766 |
ZCCHC17 |
SI00693973 |
2.1974 |
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 |
51538 |
2170 |
FABP3 |
SI00382459, 14186, SI00382445, SI00382452, esi5089, 14274, 120996, SI00382466 |
sp |
Decreased epidermal growth factor (EGF) endocytosis |
|
|
weak but specific |
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. |
|
51538 |
51538 |
ZCCHC17 |
|
-0.05 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00376-A-1 |
51538 |
51538 |
ZCCHC17 |
|
0.36323925 |
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 |
51538 |
51538 |
ZCCHC17 |
|
0.115741025 |
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 |
51538 |
|
PS1D |
|
-0.667477253 |
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 |
|
51538 |
NM_016505 |
ZCCHC17 |
|
45.397 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00386-A-1 |
51538 |
51538 |
ZCCHC17 |
|
93.9070274535022 |
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 |
51538 |
51538 |
ZCCHC17 |
|
-0.6 |
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 |