| GR00018-A-0 |
25978 |
|
CHMP2B |
v2HS_59813 |
-2.18 (0.16) |
Synthetic lethal with Ras |
|
no |
|
Synthetic lethal interaction with Ras |
A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. |
Luo et al. |
2009 |
19490893 |
Cell line |
DLD-1 |
Synthetic lethal interaction with Ras |
Micoarray hybridization |
shRNA-mir (G. Hannon) |
|
shRNA |
Log2 diff MUT-WT (and P-value) |
-0.7 (0.3) |
|
GR00053-A |
25978 |
NM_014043 |
DKFZP564O123 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
np |
1.155 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
np |
1.084 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
M-004700-00 |
3.63 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
M-004700-00 |
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 |
25978 |
ENSG00000083937 |
CHMP2B |
ENSG00000083937 |
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 |
|
GR00147-A-1 |
25978 |
25978 |
CHMP2B |
np |
np |
Decreased influenza A virus infection |
|
yes |
|
Influenza A virus infection (1) |
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. |
Brass et al. |
2009 |
20064371 |
Cell line |
U2OS |
Viral hemagglutinin protein surface expression |
Fluorescence |
siARRAY siRNA Library |
Genome-wide |
siRNA |
Percentage of viral hemagglutinin positive cells |
Complex criteria |
|
GR00147-A-2 |
25978 |
25978 |
CHMP2B |
D-004700-01 |
0.55 |
Decreased influenza A virus infection |
50 nM siRNA concentration |
no |
|
Influenza A virus infection (2) |
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. |
Brass et al. |
2009 |
20064371 |
rp |
rp |
rp |
rp |
rp |
Selected genes |
siRNA |
Percentage of infected cells |
Complex criteria |
|
GR00147-A-2 |
25978 |
25978 |
CHMP2B |
D-004700-04 |
0.39 |
Decreased influenza A virus infection |
50 nM siRNA concentration |
no |
|
Influenza A virus infection (2) |
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. |
Brass et al. |
2009 |
20064371 |
rp |
rp |
rp |
rp |
rp |
Selected genes |
siRNA |
Percentage of infected cells |
Complex criteria |
|
GR00147-A-2 |
25978 |
25978 |
CHMP2B |
D-004700-02 |
0.84 |
none |
50 nM siRNA concentration |
no |
|
Influenza A virus infection (2) |
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. |
Brass et al. |
2009 |
20064371 |
rp |
rp |
rp |
rp |
rp |
Selected genes |
siRNA |
Percentage of infected cells |
Complex criteria |
|
GR00147-A-2 |
25978 |
25978 |
CHMP2B |
D-004700-03 |
0.89 |
none |
50 nM siRNA concentration |
no |
|
Influenza A virus infection (2) |
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. |
Brass et al. |
2009 |
20064371 |
rp |
rp |
rp |
rp |
rp |
Selected genes |
siRNA |
Percentage of infected cells |
Complex criteria |
|
GR00151-A-1 |
25978 |
ENSG00000083937 |
CHMP2B |
np |
1.595 |
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 |
25978 |
25978 |
CHMP2B |
PL-50056 |
0.882 |
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 |
25978 |
NM_014043 |
CHMP2B |
M-004700-00 |
-0.247837631430981 |
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 |
25978 |
ENSG00000083937 |
|
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 |
25978 |
25978 |
CHMP2B |
M-004700-00 |
-0.810009605 |
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 |
25978 |
25978 |
CHMP2B |
M-004700-00 |
1.7149173207531 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
M-004700-00 |
1.56 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
M-004700-00 |
1.28 |
none |
|
no |
Z-score 2.893 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
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 |
25978 |
|
CHMP2B |
np |
sp |
none |
|
|
rank: 15785 |
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 |
25978 |
25978 |
DKFZP564O123 |
J-004700-09 |
1.95696 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 91.60 |
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 |
25978 |
25978 |
DKFZP564O123 |
M-004700-00 |
0.84231 |
none |
|
no |
number of cells compared to control (%): 81.59 |
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 |
25978 |
25978 |
CHMP2B |
s24862 |
-1.07822 |
none |
|
no |
number of cells compared to control (%): 85.68 |
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 |
25978 |
25978 |
CHMP2B |
s24863 |
-0.80445 |
none |
|
no |
number of cells compared to control (%): 88.12 |
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 |
25978 |
25978 |
CHMP2B |
s24864 |
-0.17016 |
none |
|
no |
number of cells compared to control (%): 97.96 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
np |
-0.321 |
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 |
25978 |
25978 |
CHMP2B |
TRCN0000128433, TRCN0000129922, TRCN0000130815, TRCN0000130897, TRCN0000131086 |
0.049887698 |
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 |
25978 |
25978 |
CHMP2B |
TRCN0000128433, TRCN0000129922, TRCN0000130815, TRCN0000130897, TRCN0000131086 |
0.389152712 |
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 |
25978 |
25978 |
CHMP2B |
TRCN0000128433, TRCN0000129922, TRCN0000130815, TRCN0000130897, TRCN0000131086 |
1.159127783 |
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 |
25978 |
25978 |
CHMP2B |
TRCN0000128433, TRCN0000129922, TRCN0000130815, TRCN0000130897, TRCN0000131086 |
0.649915989 |
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 |
25978 |
25978 |
CHMP2B |
TRCN0000128433, TRCN0000129922, TRCN0000130815, TRCN0000130897, TRCN0000131086 |
-0.688101354 |
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 |
25978 |
|
chmp2b |
124741 |
sp |
Decreased viability (cell death) |
|
|
|
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. |
GR00300-A |
25978 |
|
CHMP2B |
TRCN0000130815, TRCN0000128433, TRCN0000131086, TRCN0000129922, TRCN0000130897 |
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 |
25978 |
NM_014043 |
DKFZP564O123 |
np |
-0.71 |
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 |
25978 |
25978 |
DKFZP564O123 |
np |
-4.97 |
Decreased Sindbis virus (SINV) infection |
|
|
|
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 |
|
GR00310-A-2 |
25978 |
25978 |
CHMP2B |
124742 |
1.47 |
none |
|
|
|
Sindbis virus (SINV) infection (2) |
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 |
Selected genes |
siRNA |
Z-score |
np |
Hits identified by the curators according to the number of scoring siRNAs per gene and the top scores. |
GR00310-A-2 |
25978 |
25978 |
CHMP2B |
124740 |
-0.3 |
Decreased Sindbis virus (SINV) infection |
|
|
|
Sindbis virus (SINV) infection (2) |
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 |
Selected genes |
siRNA |
Z-score |
np |
Hits identified by the curators according to the number of scoring siRNAs per gene and the top scores. |
GR00310-A-2 |
25978 |
25978 |
CHMP2B |
124741 |
-0.11 |
Decreased Sindbis virus (SINV) infection |
|
|
|
Sindbis virus (SINV) infection (2) |
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 |
Selected genes |
siRNA |
Z-score |
np |
Hits identified by the curators according to the number of scoring siRNAs per gene and the top scores. |
|
25978 |
25978 |
CHMP2B |
np |
71.1 |
Inconclusive |
|
|
65,9% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
25978 |
NM_014043 |
DKFZP564O123 |
np |
-0.95 |
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 |
25978 |
ENSG00000083937 |
CHMP2B |
124740 |
1.2047 |
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). |
GR00363-A |
25978 |
25978 |
CHMP2B |
SI00367500, SI00367507, SI00367493, SI00367514, 124740, esi1591, 124741 |
sp |
Decreased epidermal growth factor (EGF) endocytosis |
|
|
strong |
Endocytosis regulation |
Systems survey of endocytosis by multiparametric image analysis. |
Collinet et al. |
2010 |
20190736 |
Cell line |
HeLa |
Transferrin (TF) and epidermal growth factor (EGF) subcellular localisation, DNA content |
Fluorescence |
Ambion, Qiagen and esiRNA library (Kittler et al.) |
Genome-wide |
siRNA |
Complex, sp |
Complex criteria |
Two hit categories: "strong" (maximum of Prob Chi2, Prob Chi2 EGF, Prob Chi2 Tfn > 0.95) and "weak but specific" (maximum of Prob Chi2, Prob Chi2 EGF, Prob Chi2 Tfn < 0.95 but Phenoscore > 0.95). Additional information about secondary screens with kinase and phospatase libraries. |
|
25978 |
25978 |
CHMP2B |
|
-0.04000000000000001 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00371-A-1 |
25978 |
25978 |
CHMP2B |
|
-0.0290906215103 |
none |
|
|
Ambion |
Nanog expression in absence of bFGF and TGFbeta |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-2 |
25978 |
CHMP2B |
25978 |
|
0.609728535788 |
none |
|
|
Ambion |
Nanog expression in presence of TGFbeta inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-3 |
25978 |
25978 |
CHMP2B |
|
0.0591933535443 |
none |
|
|
Ambion |
Nanog expression in presence of MEK inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-4 |
25978 |
25978 |
CHMP2B |
|
-0.0187571094277 |
none |
|
|
Ambion |
Nanog expression in presence of PI3K inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-5 |
25978 |
25978 |
CHMP2B |
|
-0.764235975962 |
none |
|
|
Ambion |
Nanog expression in presence of retinoic acid |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00376-A-1 |
25978 |
25978 |
CHMP2B |
|
0.531540099 |
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 |
25978 |
25978 |
CHMP2B |
|
0.391406321 |
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 |
|
25978 |
NM_014043 |
CHMP2B |
|
58.723 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00386-A-1 |
25978 |
25978 |
CHMP2B |
|
65.6202464165736 |
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 |
25978 |
25978 |
CHMP2B |
|
68.6 |
Decreased IL-8 secretion |
|
|
|
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 |