| Synthetic lethal interaction with Ras |
| RPS17 | |
-0.85 (0.29)
|
Synthetic lethal with Ras
| no |
ReferenceA genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Luo et al.,
2009
Oncogenic mutations in the small GTPase Ras are highly prevalent in cancer, but an understanding of the vulnerabilities of these cancers is lacking. We undertook a genome-wide RNAi screen to identify synthetic lethal interactions with the KRAS oncogene. We discovered a diverse set of proteins whose depletion selectively impaired the viability of Ras mutant cells. Among these we observed a strong enrichment for genes with mitotic functions. We describe a pathway involving the mitotic kinase PLK1, the anaphase-promoting complex/cyclosome, and the proteasome that, when inhibited, results in prometaphase accumulation and the subsequent death of Ras mutant cells. Gene expression analysis indicates that reduced expression of genes in this pathway correlates with increased survival of patients bearing tumors with a Ras transcriptional signature. Our results suggest a previously underappreciated role for Ras in mitotic progression and demonstrate a pharmacologically tractable pathway for the potential treatment of cancers harboring Ras mutations.
Screen DetailsStable ID:
GR00018-A-0
Screen Title:
Synthetic lethal interaction with Ras
Assay:
Synthetic lethal interaction with Ras
Method:
Micoarray hybridization
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
DLD1 colon adenocarcinoma cells (Ras mutant and wildtype)
Library:
, shRNA-mir (G. Hannon)
Reagent Type:
shRNA
Score Type:
Log2 diff MUT-WT (and P-value)
Cutoff:
-0.7 (0.3)
Notes:
|
| Melanogenesis | NM_001021
| RPS17 | np |
1
|
none
| no |
ReferenceGenome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. Ganesan et al.,
2008
Melanin protects the skin and eyes from the harmful effects of UV irradiation, protects neural cells from toxic insults, and is required for sound conduction in the inner ear. Aberrant regulation of melanogenesis underlies skin disorders (melasma and vitiligo), neurologic disorders (Parkinson''s disease), auditory disorders (Waardenburg''s syndrome), and opthalmologic disorders (age related macular degeneration). Much of the core synthetic machinery driving melanin production has been identified; however, the spectrum of gene products participating in melanogenesis in different physiological niches is poorly understood. Functional genomics based on RNA-mediated interference (RNAi) provides the opportunity to derive unbiased comprehensive collections of pharmaceutically tractable single gene targets supporting melanin production. In this study, we have combined a high-throughput, cell-based, one-well/one-gene screening platform with a genome-wide arrayed synthetic library of chemically synthesized, small interfering RNAs to identify novel biological pathways that govern melanin biogenesis in human melanocytes. Ninety-two novel genes that support pigment production were identified with a low false discovery rate. Secondary validation and preliminary mechanistic studies identified a large panel of targets that converge on tyrosinase expression and stability. Small molecule inhibition of a family of gene products in this class was sufficient to impair chronic tyrosinase expression in pigmented melanoma cells and UV-induced tyrosinase expression in primary melanocytes. Isolation of molecular machinery known to support autophagosome biosynthesis from this screen, together with in vitro and in vivo validation, exposed a close functional relationship between melanogenesis and autophagy. In summary, these studies illustrate the power of RNAi-based functional genomics to identify novel genes, pathways, and pharmacologic agents that impact a biological phenotype and operate outside of preconceived mechanistic relationships.
Screen DetailsStable ID:
GR00056-A
Screen Title:
Melanogenesis
Assay:
Melanin protein expression and viability
Method:
Absorbance and luminescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
MNT-1
Library:
Dharmacon, rp
Reagent Type:
siRNA
Score Type:
Normalized absorbance ratio
Cutoff:
> 2 standard deviations below mean
Notes:
Additional information about a secondary screen (retest to determine false-positive rate)
|
| Cell division (3) | ENSG00000184779
| RPS17 | ENSG00000184779 |
-1,6
|
none
| yes |
ReferenceGenome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al.,
2007
Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Screen DetailsStable ID:
GR00098-A-3
Screen Title:
Cell division (3)
Assay:
Histone H3 phosphorylation; alpha-tubulin and pericentrin protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Mitotic index
Cutoff:
>= 2
Notes:
|
| Ribosome biogenesis (2) | NM_001021
| RPS17 | np |
sp
|
Cytoplasmic 40S maturation defects
| yes |
ReferenceA protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. Wild et al.,
2010
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
Screen DetailsStable ID:
GR00209-A-2
Screen Title:
Ribosome biogenesis (2)
Assay:
Enp1 protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Qiagen, np
Reagent Type:
siRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
|
| Cell division (1) | ENSG00000184779
| RPS17 | ENSG00000184779 |
sp
|
Increased S DNA content
| yes |
ReferenceGenome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al.,
2007
Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Screen DetailsStable ID:
GR00098-A-1
Screen Title:
Cell division (1)
Assay:
Cell number and DNA content
Method:
Laser scanning cytometry
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
|
| Human papillomavirus oncogene expression regulation (1) | 6218
| RPS17 | |
-1,55
|
none
| no |
ReferenceGenome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. Smith et al.,
2010
An essential step in the pathogenesis of human papillomavirus (HPV)-associated cancers is the dysregulated expression of the viral oncogenes. The papillomavirus E2 protein can silence the long control region (LCR) promoter that controls viral E6 and E7 oncogene expression. The mechanisms by which E2 represses oncogene expression and the cellular factors through which E2 mediates this silencing are largely unknown. We conducted an unbiased, genome-wide siRNA screen and series of secondary screens that identified 96 cellular genes that contribute to the repression of the HPV LCR. In addition to confirming a role for the E2-binding bromodomain protein Brd4 in E2-mediated silencing, we identified a number of genes that have not previously been implicated in E2 repression, including the demethylase JARID1C/SMCX as well as EP400, a component of the NuA4/TIP60 histone acetyltransferase complex. Each of these genes contributes independently and additively to E2-mediated silencing, indicating that E2 functions through several distinct cellular complexes to repress E6 and E7 expression.
Screen DetailsStable ID:
GR00197-A-1
Screen Title:
Human papillomavirus oncogene expression regulation (1)
Assay:
HPV18 LCR reporter activity
Method:
Luminescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
C33A/BE2/18LCR c4
Library:
Dharmacon, Human siGENOME SMARTpool library
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
>= 2
Notes:
Author-submitted data; Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5
|
| Ribosome biogenesis (1) | NM_001021
| RPS17 | np |
0,63
|
Nucleolar pre-40S maturation defects
| yes |
ReferenceA protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. Wild et al.,
2010
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
Screen DetailsStable ID:
GR00209-A-1
Screen Title:
Ribosome biogenesis (1)
Assay:
Rps2 protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Qiagen, np
Reagent Type:
siRNA
Score Type:
Average relative rank from >= 2 siRNAs
Cutoff:
> 0.2
Notes:
|
| Ribosome biogenesis (3) | NM_001021
| RPS17 | np |
np
|
none
| yes |
ReferenceA protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. Wild et al.,
2010
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
Screen DetailsStable ID:
GR00209-A-3
Screen Title:
Ribosome biogenesis (3)
Assay:
Rpl29 protein expression
Method:
Fluorescence
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Qiagen, np
Reagent Type:
siRNA
Score Type:
Average relative rank from >= 2 siRNAs
Cutoff:
> 0.25
Notes:
|
| Cell viability |
| RPS17 | np |
12
|
Decreased viability
| no |
ReferenceHighly parallel identification of essential genes in cancer cells. Luo et al.,
2008
More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the structural basis of cancer, by identifying the genomic mutations associated with each cancer type. A powerful complementary approach is to systematically characterize the functional basis of cancer, by identifying the genes essential for growth and related phenotypes in different cancer cells. Such information would be particularly valuable for identifying potential drug targets. Here, we report the development of an efficient, robust approach to perform genome-scale pooled shRNA screens for both positive and negative selection and its application to systematically identify cell essential genes in 12 cancer cell lines. By integrating these functional data with comprehensive genetic analyses of primary human tumors, we identified known and putative oncogenes such as EGFR, KRAS, MYC, BCR-ABL, MYB, CRKL, and CDK4 that are essential for cancer cell proliferation and also altered in human cancers. We further used this approach to identify genes involved in the response of cancer cells to tumoricidal agents and found 4 genes required for the response of CML cells to imatinib treatment: PTPN1, NF1, SMARCB1, and SMARCE1, and 5 regulators of the response to FAS activation, FAS, FADD, CASP8, ARID1A and CBX1. Broad application of this highly parallel genetic screening strategy will not only facilitate the rapid identification of genes that drive the malignant state and its response to therapeutics but will also enable the discovery of genes that participate in any biological process.
Screen DetailsStable ID:
GR00106-A-0
Screen Title:
Cell viability
Assay:
Cell viability
Method:
Micoarray hybridization
Scope:
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
12 cancer cell lines
Library:
, TRC shRNA library
Reagent Type:
shRNA
Score Type:
Essentiality
Cutoff:
>= 8/12 cancer cell lines
Notes:
|
| Self-renewal and pluripotency in human embryonic stem cells (1) | NM_001021
| RPS17 | |
0,09
|
none
| no |
ReferenceA genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al.,
2010
The derivation of human ES cells (hESCs) from human blastocysts represents one of the milestones in stem cell biology. The full potential of hESCs in research and clinical applications requires a detailed understanding of the genetic network that governs the unique properties of hESCs. Here, we report a genome-wide RNA interference screen to identify genes which regulate self-renewal and pluripotency properties in hESCs. Interestingly, functionally distinct complexes involved in transcriptional regulation and chromatin remodelling are among the factors identified in the screen. To understand the roles of these potential regulators of hESCs, we studied transcription factor PRDM14 to gain new insights into its functional roles in the regulation of pluripotency. We showed that PRDM14 regulates directly the expression of key pluripotency gene POU5F1 through its proximal enhancer. Genome-wide location profiling experiments revealed that PRDM14 colocalized extensively with other key transcription factors such as OCT4, NANOG and SOX2, indicating that PRDM14 is integrated into the core transcriptional regulatory network. More importantly, in a gain-of-function assay, we showed that PRDM14 is able to enhance the efficiency of reprogramming of human fibroblasts in conjunction with OCT4, SOX2 and KLF4. Altogether, our study uncovers a wealth of novel hESC regulators wherein PRDM14 exemplifies a key transcription factor required for the maintenance of hESC identity and the reacquisition of pluripotency in human somatic cells.
Screen DetailsStable ID:
GR00184-A-1
Screen Title:
Self-renewal and pluripotency in human embryonic stem cells (1)
Assay:
POU5F1 protein expression
Method:
Fluorescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
hESC H1
Library:
Dharmacon, SMARTpool siRNA library
Reagent Type:
siRNA
Score Type:
Z-score
Cutoff:
< -2
Notes:
|
| Cell division (1) | ENSG00000198235
| RPS17 | ENSG00000198235 |
sp
|
Increased S DNA content
| no |
ReferenceGenome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al.,
2007
Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Screen DetailsStable ID:
GR00098-A-1
Screen Title:
Cell division (1)
Assay:
Cell number and DNA content
Method:
Laser scanning cytometry
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
|
| Combinatorial effect with paclitaxel | NM_001021
| RPS17 | np |
1,02
|
none
| no |
ReferenceSynthetic lethal screen identification of chemosensitizer loci in cancer cells. Whitehurst et al.,
2007
Abundant evidence suggests that a unifying principle governing the molecular pathology of cancer is the co-dependent aberrant regulation of core machinery driving proliferation and suppressing apoptosis. Anomalous proteins engaged in support of this tumorigenic regulatory environment most probably represent optimal intervention targets in a heterogeneous population of cancer cells. The advent of RNA-mediated interference (RNAi)-based functional genomics provides the opportunity to derive unbiased comprehensive collections of validated gene targets supporting critical biological systems outside the framework of preconceived notions of mechanistic relationships. We have combined a high-throughput cell-based one-well/one-gene screening platform with a genome-wide synthetic library of chemically synthesized small interfering RNAs for systematic interrogation of the molecular underpinnings of cancer cell chemoresponsiveness. NCI-H1155, a human non-small-cell lung cancer line, was employed in a paclitaxel-dependent synthetic lethal screen designed to identify gene targets that specifically reduce cell viability in the presence of otherwise sublethal concentrations of paclitaxel. Using a stringent objective statistical algorithm to reduce false discovery rates below 5%, we isolated a panel of 87 genes that represent major focal points of the autonomous response of cancer cells to the abrogation of microtubule dynamics. Here we show that several of these targets sensitize lung cancer cells to paclitaxel concentrations 1,000-fold lower than otherwise required for a significant response, and we identify mechanistic relationships between cancer-associated aberrant gene expression programmes and the basic cellular machinery required for robust mitotic progression.
Screen DetailsStable ID:
GR00054-A
Screen Title:
Combinatorial effect with paclitaxel
Assay:
Viability (synthetic lethal)
Method:
ATP level
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
NCI-H1155
Library:
Dharmacon, # G-005000-01
Reagent Type:
siRNA
Score Type:
Paclitaxel/control ratio
Cutoff:
Complex criteria
Notes:
Additional information about 87 high-confidence hits
|
| Genome stability | NM_001021
| RPS17 | np |
sp
|
none
| no |
ReferenceA genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Paulsen et al.,
2009
Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated.
Screen DetailsStable ID:
GR00053-A
Screen Title:
Genome stability
Assay:
gamma-H2AX phosphorylation and DNA content
Method:
Fluorescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
ThermoFisher Scientific, siARRAY human genome siRNA library
Reagent Type:
siRNA
Score Type:
p-value
Cutoff:
Complex criteria
Notes:
Confidence groupings from 4 to 1 (highest level of confidence in group 4)
|
| Cell division (4) | ENSG00000184779
| RPS17 | ENSG00000184779 |
-4,6
|
none
| no |
ReferenceGenome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al.,
2007
Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Screen DetailsStable ID:
GR00098-A-4
Screen Title:
Cell division (4)
Assay:
Cell size (forward scatter)
Method:
Flow cytometry
Scope:
Selected genes
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Cell size
Cutoff:
>= 2
Notes:
|
| Hepatitis C virus replication (1) | 6218
| RPS17 | PL-50050 |
0,8
|
none
| no |
ReferenceA functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Tai et al.,
2009
Hepatitis C virus (HCV) chronically infects 3% of the world''s population, and complications from HCV are the leading indication for liver transplantation. Given the need for better anti-HCV therapies, one strategy is to identify and target cellular cofactors of the virus lifecycle. Using a genome-wide siRNA library, we identified 96 human genes that support HCV replication, with a significant number of them being involved in vesicle organization and biogenesis. Phosphatidylinositol 4-kinase PI4KA and multiple subunits of the COPI vesicle coat complex were among the genes identified. Consistent with this, pharmacologic inhibitors of COPI and PI4KA blocked HCV replication. Targeting hepcidin, a peptide critical for iron homeostasis, also affected HCV replication, which may explain the known dysregulation of iron homeostasis in HCV infection. The host cofactors for HCV replication identified in this study should serve as a useful resource in delineating new targets for anti-HCV therapies.
Screen DetailsStable ID:
GR00180-A-1
Screen Title:
Hepatitis C virus replication (1)
Assay:
HCV replicon RNA copy number
Method:
Luminescence
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
Huh7/Rep-Feo
Library:
Dharmacon, siARRAY Human Genome siRNA Library
Reagent Type:
siRNA
Score Type:
q-value
Cutoff:
Complex criteria
Notes:
|
| Cell division (1) | ENSG00000197575
| RPS17 | ENSG00000197575 |
sp
|
none
| no |
ReferenceGenome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al.,
2007
Cell division is fundamental for all organisms. Here we report a genome-scale RNA-mediated interference screen in HeLa cells designed to identify human genes that are important for cell division. We have used a library of endoribonuclease-prepared short interfering RNAs for gene silencing and have used DNA content analysis to identify genes that induced cell cycle arrest or altered ploidy on silencing. Validation and secondary assays were performed to generate a nine-parameter loss-of-function phenoprint for each of the genes. These phenotypic signatures allowed the assignment of genes to specific functional classes by combining hierarchical clustering, cross-species analysis and proteomic data mining. We highlight the richness of our dataset by ascribing novel functions to genes in mitosis and cytokinesis. In particular, we identify two evolutionarily conserved transcriptional regulatory networks that govern cytokinesis. Our work provides an experimental framework from which the systematic analysis of novel genes necessary for cell division in human cells can begin.
Screen DetailsStable ID:
GR00098-A-1
Screen Title:
Cell division (1)
Assay:
Cell number and DNA content
Method:
Laser scanning cytometry
Scope:
Genome-wide
Screen Type:
Cell-based
Species:
Homo sapiens
Biosource:
Cell line
Biomodel:
HeLa
Library:
Custom-made, rp
Reagent Type:
esiRNA
Score Type:
Complex, sp
Cutoff:
Complex criteria
Notes:
|