GenomeRNAi

Phenotype information for gene 318206 (tlk)

Screen Title	Gene ID	Gene Symbol	Reagent ID	Score	Phenotype	Follow Up
Notch pathway regulation (4)	CG34412		46426	sp	Completely lethal (pupal)	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Actin organization and cell morphology (3)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	Altered cell morphology	yes
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-3 Screen title: Actin organization and cell morphology (3) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Mitochondrial Ca2+ and H+ regulation	FBgn0086899		DRSC22926		2	no
Reference Genome-wide RNAi screen identifies Letm1 as a mitochondrial Ca2+/H+ antiporter. Jiang et al., 2009 Mitochondria are integral components of cellular calcium (Ca2+) signaling. Calcium stimulates mitochondrial adenosine 5''-triphosphate production, but can also initiate apoptosis. In turn, cytoplasmic Ca2+ concentrations are regulated by mitochondria. Although several transporter and ion-channel mechanisms have been measured in mitochondria, the molecules that govern Ca2+ movement across the inner mitochondrial membrane are unknown. We searched for genes that regulate mitochondrial Ca2+ and H+ concentrations using a genome-wide Drosophila RNA interference (RNAi) screen. The mammalian homolog of one Drosophila gene identified in the screen, Letm1, was found to specifically mediate coupled Ca2+/H+ exchange. RNAi knockdown, overexpression, and liposome reconstitution of the purified Letm1 protein demonstrate that Letm1 is a mitochondrial Ca2+/H+ antiporter. View Phenotypes Download PubMed Screen details Stable Id: GR00131-A-0 Screen title: Mitochondrial Ca2+ and H+ regulation Assay: Mitochondrial Ca2+ transport Method: Mitochondrial (Mt)-pericam emission Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 (stably transfected with mitochondria-targeted ratiometric pericam) Library: , DRSC Reagent type: dsRNA Score type: Percent positive control Cutoff: >= 25% (1), >= 50% (2), >= 75% (3) Notes:
Lipid storage	FBgn0052781		DRSC22938	0.51	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Lipid storage	FBgn0026698		DRSC22926	-3.66	Lipid understorage	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Notch induced transcription	CG32782	tlk	np	-2.4	Downregulation of Notch pathway after Notch stimulation	yes
Reference Modifiers of notch transcriptional activity identified by genome-wide RNAi. Mourikis et al., 2010 The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. View Phenotypes Download PubMed Screen details Stable Id: GR00152-A Screen title: Notch induced transcription Assay: Notch pathway reporter Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: DRSC, np Reagent type: dsRNA Score type: Z-score Cutoff: < -2 OR > 2 (con-luc) OR < -1.8 OR > 1.8 (m3-luc) Notes: Additional information about secondary screens
Cell size and cell-cycle regulation (1)	FBgn0051025\|FBgn0052782	CG31025\|CG32782	AT12465	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Actin organization and cell morphology (1)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	Altered cell morphology	yes
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-1 Screen title: Actin organization and cell morphology (1) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0004102\|FBgn0052782	oc\|CG32782	RE10280	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
ERK signaling	FBgn0086899		DRSC22926	weak	ERK activation reduced	no
Reference A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Friedman et al., 2006 Receptor tyrosine kinase (RTK) signalling through extracellular-signal-regulated kinases (ERKs) has pivotal roles during metazoan development, underlying processes as diverse as fate determination, differentiation, proliferation, survival, migration and growth. Abnormal RTK/ERK signalling has been extensively documented to contribute to developmental disorders and disease, most notably in oncogenic transformation by mutant RTKs or downstream pathway components such as Ras and Raf. Although the core RTK/ERK signalling cassette has been characterized by decades of research using mammalian cell culture and forward genetic screens in model organisms, signal propagation through this pathway is probably regulated by a larger network of moderate, context-specific proteins. The genes encoding these proteins may not have been discovered through traditional screens owing, in particular, to the requirement for visible phenotypes. To obtain a global view of RTK/ERK signalling, we performed an unbiased, RNA interference (RNAi), genome-wide, high-throughput screen in Drosophila cells using a novel, quantitative, cellular assay monitoring ERK activation. Here we show that ERK pathway output integrates a wide array of conserved cellular processes. Further analysis of selected components-in multiple cell types with different RTK ligands and oncogenic stimuli-validates and classifies 331 pathway regulators. The relevance of these genes is highlighted by our isolation of a Ste20-like kinase and a PPM-family phosphatase that seem to regulate RTK/ERK signalling in vivo and in mammalian cells. Novel regulators that modulate specific pathway outputs may be selective targets for drug discovery. View Phenotypes Download PubMed Screen details Stable Id: GR00021-A-0 Screen title: ERK signaling Assay: ERK signaling Method: Fluorescence Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2R+ Library: , DRSC Reagent type: dsRNA Score type: Weak, moderate, strong Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0052782	CG32782	AT22150	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell growth and viability (1)			HFA17731	1.4	none	yes
Reference Genome-wide RNAi analysis of growth and viability in Drosophila cells. Boutros et al., 2004 A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale. View Phenotypes Download PubMed Screen details Stable Id: GR00031-A-1 Screen title: Cell growth and viability (1) Assay: Cell number and viability Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: Custom-made, HFA Reagent type: dsRNA Score type: Z-score Cutoff: >= 3.0 Notes:
Lipid storage			DRSC17731	1.16	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
G2-M DNA damage checkpoint regulation (1)		tlk\|nbs	DRSC22926 custom (nbs)	np	Increased histone H3 phosphorylation with doxorubicin	no
Reference A genome-wide RNAi screen identifies core components of the G₂-M DNA damage checkpoint. Kondo and Perrimon, 2011 The DNA damage checkpoint, the first pathway known to be activated in response to DNA damage, is a mechanism by which the cell cycle is temporarily arrested to allow DNA repair. The checkpoint pathway transmits signals from the sites of DNA damage to the cell cycle machinery through the evolutionarily conserved ATM (ataxia telangiectasia mutated) and ATR (ATM- and Rad3-related) kinase cascades. We conducted a genome-wide RNAi (RNA interference) screen in Drosophila cells to identify previously unknown genes and pathways required for the G₂-M checkpoint induced by DNA double-strand breaks (DSBs). Our large-scale analysis provided a systems-level view of the G₂-M checkpoint and revealed the coordinated actions of particular classes of proteins, which include those involved in DNA repair, DNA replication, cell cycle control, chromatin regulation, and RNA processing. Further, from the screen and in vivo analysis, we identified previously unrecognized roles of two DNA damage response genes, mus101 and mus312. Our results suggest that the DNA replication preinitiation complex, which includes MUS101, and the MUS312-containing nuclease complexes, which are important for DSB repair, also function in the G₂-M checkpoint. Our results provide insight into the diverse mechanisms that link DNA damage and the checkpoint signaling pathway. View Phenotypes Download PubMed Screen details Stable Id: GR00172-A-1 Screen title: G2-M DNA damage checkpoint regulation (1) Assay: Histone H3 phosphorylation Method: Fluorescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2R+ Library: DRSC and custom-made, DRSC 2.0 and custom-made Reagent type: dsRNA Score type: Mitotic cell number per well Cutoff: > 20 Notes:
Cell size and cell-cycle regulation (1)	FBgn0036900\|FBgn0052782	CG32782\|CG8765	GM03003	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0039570\|FBgn0052782	CG32782\|CG12870	np	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Combinatorial effect with methyl methanesulphonate (1)	FBgn0086899	CG34412	DRSC22926	sp	Synthetic lethal with methyl methanesulphonate	no
Reference A network of conserved damage survival pathways revealed by a genomic RNAi screen. Ravi et al., 2009 Damage initiates a pleiotropic cellular response aimed at cellular survival when appropriate. To identify genes required for damage survival, we used a cell-based RNAi screen against the Drosophila genome and the alkylating agent methyl methanesulphonate (MMS). Similar studies performed in other model organisms report that damage response may involve pleiotropic cellular processes other than the central DNA repair components, yet an intuitive systems level view of the cellular components required for damage survival, their interrelationship, and contextual importance has been lacking. Further, by comparing data from different model organisms, identification of conserved and presumably core survival components should be forthcoming. We identified 307 genes, representing 13 signaling, metabolic, or enzymatic pathways, affecting cellular survival of MMS-induced damage. As expected, the majority of these pathways are involved in DNA repair; however, several pathways with more diverse biological functions were also identified, including the TOR pathway, transcription, translation, proteasome, glutathione synthesis, ATP synthesis, and Notch signaling, and these were equally important in damage survival. Comparison with genomic screen data from Saccharomyces cerevisiae revealed no overlap enrichment of individual genes between the species, but a conservation of the pathways. To demonstrate the functional conservation of pathways, five were tested in Drosophila and mouse cells, with each pathway responding to alkylation damage in both species. Using the protein interactome, a significant level of connectivity was observed between Drosophila MMS survival proteins, suggesting a higher order relationship. This connectivity was dramatically improved by incorporating the components of the 13 identified pathways within the network. Grouping proteins into "pathway nodes" qualitatively improved the interactome organization, revealing a highly organized "MMS survival network." We conclude that identification of pathways can facilitate comparative biology analysis when direct gene/orthologue comparisons fail. A biologically intuitive, highly interconnected MMS survival network was revealed after we incorporated pathway data in our interactome analysis. View Phenotypes Download PubMed Screen details Stable Id: GR00128-A-1 Screen title: Combinatorial effect with methyl methanesulphonate (1) Assay: Viability (synthetic lethal) Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: DRSC, Version 1 Reagent type: dsRNA Score type: rp Cutoff: rp Notes: Additional information about the primary screen
Lipid storage	FBgn0052781		DRSC23163	-1.15	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Cell size and cell-cycle regulation (1)	FBgn0022800\|FBgn0052782	Cad96Ca\|CG32782	SD07683	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0030069\|FBgn0052782	CG12660\|CG32782	RH08828	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Drosophila small RNA pathways		tlk	DRSC22926	0.5	miRNA reporter downregulated	no
Reference Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Zhou et al., 2008 The specificity of RNAi pathways is determined by several classes of small RNAs, which include siRNAs, piRNAs, endo-siRNAs, and microRNAs (miRNAs). These small RNAs are invariably incorporated into large Argonaute (Ago)-containing effector complexes known as RNA-induced silencing complexes (RISCs), which they guide to silencing targets. Both genetic and biochemical strategies have yielded conserved molecular components of small RNA biogenesis and effector machineries. However, given the complexity of these pathways, there are likely to be additional components and regulators that remain to be uncovered. We have undertaken a comparative and comprehensive RNAi screen to identify genes that impact three major Ago-dependent small RNA pathways that operate in Drosophila S2 cells. We identify subsets of candidates that act positively or negatively in siRNA, endo-siRNA, and miRNA pathways. Our studies indicate that many components are shared among all three Argonaute-dependent silencing pathways, though each is also impacted by discrete sets of genes. View Phenotypes Download PubMed Screen details Stable Id: GR00004-A-0 Screen title: Drosophila small RNA pathways Assay: miRNA and siRNA pathway activity Method: Dual luciferase Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , DRSC Reagent type: dsRNA Score type: Fold change endo-siRNA reporter Cutoff: 1.5/0.6 Notes:
Cell morphology	FBgn0086899	BcDNA:GH07910	np	np	Morphology	no
Reference A functional genomic analysis of cell morphology using RNA interference. Kiger et al., 2003 The diversity of metazoan cell shapes is influenced by the dynamic cytoskeletal network. With the advent of RNA-interference (RNAi) technology, it is now possible to screen systematically for genes controlling specific cell-biological processes, including those required to generate distinct morphologies. View Phenotypes Download PubMed Screen details Stable Id: GR00026-A-0 Screen title: Cell morphology Assay: Morphology Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167, S2R+ Library: , Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0028397\|FBgn0052782	Tob\|CG32782	LD04013	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Lipid storage			DRSC17731	0.19	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Serratia marcescens infection (1)	CG32781	CG32781	46424	0.15	none	no
Reference Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al., 2009 Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity. View Phenotypes Download PubMed Screen details Stable Id: GR00142-A-1 Screen title: Serratia marcescens infection (1) Assay: Heat shock and viability Method: Fly count Scope: Random genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: HSP70-GAL4; TubGAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Days life time (LT50) Cutoff: < -1.5 SD OR > 2 SD Notes:
Adiposity regulation (1)	FBgn0086899	tlk	46425	-0.11	none	no
Reference Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Pospisilik et al., 2010 Over 1 billion people are estimated to be overweight, placing them at risk for diabetes, cardiovascular disease, and cancer. We performed a systems-level genetic dissection of adiposity regulation using genome-wide RNAi screening in adult Drosophila. As a follow-up, the resulting approximately 500 candidate obesity genes were functionally classified using muscle-, oenocyte-, fat-body-, and neuronal-specific knockdown in vivo and revealed hedgehog signaling as the top-scoring fat-body-specific pathway. To extrapolate these findings into mammals, we generated fat-specific hedgehog-activation mutant mice. Intriguingly, these mice displayed near total loss of white, but not brown, fat compartments. Mechanistically, activation of hedgehog signaling irreversibly blocked differentiation of white adipocytes through direct, coordinate modulation of early adipogenic factors. These findings identify a role for hedgehog signaling in white/brown adipocyte determination and link in vivo RNAi-based scanning of the Drosophila genome to regulation of adipocyte cell fate in mammals. View Phenotypes Download PubMed Screen details Stable Id: GR00190-A-1 Screen title: Adiposity regulation (1) Assay: Total fly triglyceride expression Method: Colorimetric determination Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: Hsp70-GAL4;Tub-GAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Triglyceride change Cutoff: Z-score > 1.65 after 3 screening rounds Notes: Additional information about the primary screen
Heat nociception (1)	CG32782	tlk	46426	-1.17	none	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Heat nociception (1)	CG12462	tlk	7025	-0.66	none	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Lipid storage	FBgn0029675		DRSC17835	-0.13	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Heat nociception (1)	CG12462	Smr	7025	-0.66	none	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Lipid storage	FBgn0086899	CG32782	np	strong	Fewer lipid droplets	no
Reference Functional genomic screen reveals genes involved in lipid-droplet formation and utilization. Guo et al., 2008 Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets enclosed in a monolayer of phospholipids and associated proteins. These dynamic organelles serve as the principal reservoirs for storing cellular energy and for the building blocks for membrane lipids. Excessive lipid accumulation in cells is a central feature of obesity, diabetes and atherosclerosis, yet remarkably little is known about lipid-droplet cell biology. Here we show, by means of a genome-wide RNA interference (RNAi) screen in Drosophila S2 cells that about 1.5% of all genes function in lipid-droplet formation and regulation. The phenotypes of the gene knockdowns sorted into five distinct phenotypic classes. Genes encoding enzymes of phospholipid biosynthesis proved to be determinants of lipid-droplet size and number, suggesting that the phospholipid composition of the monolayer profoundly affects droplet morphology and lipid utilization. A subset of the Arf1-COPI vesicular transport proteins also regulated droplet morphology and lipid utilization, thereby identifying a previously unrecognized function for this machinery. These phenotypes are conserved in mammalian cells, suggesting that insights from these studies are likely to be central to our understanding of human diseases involving excessive lipid storage. View Phenotypes Download PubMed Screen details Stable Id: GR00090-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , OpenBiosystems Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Notch pathway regulation (4)	CG4013\|CG34412		7026	sp	Completely lethal (pupal)	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Lipid storage	FBgn0026698		DRSC22924	-2.95	Lipid understorage	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Adiposity regulation (1)		CG32781	46424	-0.15	none	no
Reference Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Pospisilik et al., 2010 Over 1 billion people are estimated to be overweight, placing them at risk for diabetes, cardiovascular disease, and cancer. We performed a systems-level genetic dissection of adiposity regulation using genome-wide RNAi screening in adult Drosophila. As a follow-up, the resulting approximately 500 candidate obesity genes were functionally classified using muscle-, oenocyte-, fat-body-, and neuronal-specific knockdown in vivo and revealed hedgehog signaling as the top-scoring fat-body-specific pathway. To extrapolate these findings into mammals, we generated fat-specific hedgehog-activation mutant mice. Intriguingly, these mice displayed near total loss of white, but not brown, fat compartments. Mechanistically, activation of hedgehog signaling irreversibly blocked differentiation of white adipocytes through direct, coordinate modulation of early adipogenic factors. These findings identify a role for hedgehog signaling in white/brown adipocyte determination and link in vivo RNAi-based scanning of the Drosophila genome to regulation of adipocyte cell fate in mammals. View Phenotypes Download PubMed Screen details Stable Id: GR00190-A-1 Screen title: Adiposity regulation (1) Assay: Total fly triglyceride expression Method: Colorimetric determination Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: Hsp70-GAL4;Tub-GAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Triglyceride change Cutoff: Z-score > 1.65 after 3 screening rounds Notes: Additional information about the primary screen
Notch induced transcription	CG32782	tlk	np	-2.2	none	yes
Reference Modifiers of notch transcriptional activity identified by genome-wide RNAi. Mourikis et al., 2010 The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. View Phenotypes Download PubMed Screen details Stable Id: GR00152-A Screen title: Notch induced transcription Assay: Notch pathway reporter Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: DRSC, np Reagent type: dsRNA Score type: Z-score Cutoff: < -2 OR > 2 (con-luc) OR < -1.8 OR > 1.8 (m3-luc) Notes: Additional information about secondary screens
Lipid storage	FBgn0086899		tlk	np	Understorage	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Cell size and cell-cycle regulation (1)	FBgn0016694\|FBgn0052782	Pdp1\|CG32782	LD15160	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0028489	CG2829	CT9593	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell growth and viability (2)			HFA17731	1.9	none	no
Reference Genome-wide RNAi analysis of growth and viability in Drosophila cells. Boutros et al., 2004 A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale. View Phenotypes Download PubMed Screen details Stable Id: GR00031-A-2 Screen title: Cell growth and viability (2) Assay: Cell number and viability Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2R+ Library: Custom-made, HFA Reagent type: dsRNA Score type: Z-score Cutoff: >= 3.0 Notes:
Actin organization and cell morphology (5)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	none	yes
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-5 Screen title: Actin organization and cell morphology (5) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: BG3-c1 Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Lipid storage	FBgn0052781		DRSC22938	-0.97	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Mitochondrial Ca2+ and H+ regulation	FBgn0086899		DRSC17731		2	no
Reference Genome-wide RNAi screen identifies Letm1 as a mitochondrial Ca2+/H+ antiporter. Jiang et al., 2009 Mitochondria are integral components of cellular calcium (Ca2+) signaling. Calcium stimulates mitochondrial adenosine 5''-triphosphate production, but can also initiate apoptosis. In turn, cytoplasmic Ca2+ concentrations are regulated by mitochondria. Although several transporter and ion-channel mechanisms have been measured in mitochondria, the molecules that govern Ca2+ movement across the inner mitochondrial membrane are unknown. We searched for genes that regulate mitochondrial Ca2+ and H+ concentrations using a genome-wide Drosophila RNA interference (RNAi) screen. The mammalian homolog of one Drosophila gene identified in the screen, Letm1, was found to specifically mediate coupled Ca2+/H+ exchange. RNAi knockdown, overexpression, and liposome reconstitution of the purified Letm1 protein demonstrate that Letm1 is a mitochondrial Ca2+/H+ antiporter. View Phenotypes Download PubMed Screen details Stable Id: GR00131-A-0 Screen title: Mitochondrial Ca2+ and H+ regulation Assay: Mitochondrial Ca2+ transport Method: Mitochondrial (Mt)-pericam emission Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 (stably transfected with mitochondria-targeted ratiometric pericam) Library: , DRSC Reagent type: dsRNA Score type: Percent positive control Cutoff: >= 25% (1), >= 50% (2), >= 75% (3) Notes:
Heat nociception (1)	CG32781	CG32781	46424	-0.1	none	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Cell size and cell-cycle regulation (1)	FBgn0033856\|FBgn0052782	CG32782\|CG13334	AT22132	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Drosophila small RNA pathways		tlk	DRSC22926	0.3	Endo-siRNA reporter downregulated	no
Reference Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Zhou et al., 2008 The specificity of RNAi pathways is determined by several classes of small RNAs, which include siRNAs, piRNAs, endo-siRNAs, and microRNAs (miRNAs). These small RNAs are invariably incorporated into large Argonaute (Ago)-containing effector complexes known as RNA-induced silencing complexes (RISCs), which they guide to silencing targets. Both genetic and biochemical strategies have yielded conserved molecular components of small RNA biogenesis and effector machineries. However, given the complexity of these pathways, there are likely to be additional components and regulators that remain to be uncovered. We have undertaken a comparative and comprehensive RNAi screen to identify genes that impact three major Ago-dependent small RNA pathways that operate in Drosophila S2 cells. We identify subsets of candidates that act positively or negatively in siRNA, endo-siRNA, and miRNA pathways. Our studies indicate that many components are shared among all three Argonaute-dependent silencing pathways, though each is also impacted by discrete sets of genes. View Phenotypes Download PubMed Screen details Stable Id: GR00004-A-0 Screen title: Drosophila small RNA pathways Assay: miRNA and siRNA pathway activity Method: Dual luciferase Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , DRSC Reagent type: dsRNA Score type: Fold change endo-siRNA reporter Cutoff: 1.5/0.6 Notes:
Heart development and function (1)	CG32782		46426	0.75	none	no
Reference A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function. Neely et al., 2010 Heart diseases are the most common causes of morbidity and death in humans. Using cardiac-specific RNAi-silencing in Drosophila, we knocked down 7061 evolutionarily conserved genes under conditions of stress. We present a first global roadmap of pathways potentially playing conserved roles in the cardiovascular system. One critical pathway identified was the CCR4-Not complex implicated in transcriptional and posttranscriptional regulatory mechanisms. Silencing of CCR4-Not components in adult Drosophila resulted in myofibrillar disarray and dilated cardiomyopathy. Heterozygous not3 knockout mice showed spontaneous impairment of cardiac contractility and increased susceptibility to heart failure. These heart defects were reversed via inhibition of HDACs, suggesting a mechanistic link to epigenetic chromatin remodeling. In humans, we show that a common NOT3 SNP correlates with altered cardiac QT intervals, a known cause of potentially lethal ventricular tachyarrhythmias. Thus, our functional genome-wide screen in Drosophila can identify candidates that directly translate into conserved mammalian genes involved in heart function. View Phenotypes Download PubMed Screen details Stable Id: GR00138-A-1 Screen title: Heart development and function (1) Assay: Viability Method: Fly count Scope: Selected genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: TinCΔ4 12a-Gal4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Developmental lethality Cutoff: <= 0.6666 Notes:
Cell size and cell-cycle regulation (1)	FBgn0053070\|FBgn0052782	CG33070\|CG32782	GH23165	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Adiposity regulation (1)	FBgn0086899	tlk	7025	-0.38	Decreased triglyceride expression	no
Reference Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Pospisilik et al., 2010 Over 1 billion people are estimated to be overweight, placing them at risk for diabetes, cardiovascular disease, and cancer. We performed a systems-level genetic dissection of adiposity regulation using genome-wide RNAi screening in adult Drosophila. As a follow-up, the resulting approximately 500 candidate obesity genes were functionally classified using muscle-, oenocyte-, fat-body-, and neuronal-specific knockdown in vivo and revealed hedgehog signaling as the top-scoring fat-body-specific pathway. To extrapolate these findings into mammals, we generated fat-specific hedgehog-activation mutant mice. Intriguingly, these mice displayed near total loss of white, but not brown, fat compartments. Mechanistically, activation of hedgehog signaling irreversibly blocked differentiation of white adipocytes through direct, coordinate modulation of early adipogenic factors. These findings identify a role for hedgehog signaling in white/brown adipocyte determination and link in vivo RNAi-based scanning of the Drosophila genome to regulation of adipocyte cell fate in mammals. View Phenotypes Download PubMed Screen details Stable Id: GR00190-A-1 Screen title: Adiposity regulation (1) Assay: Total fly triglyceride expression Method: Colorimetric determination Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: Hsp70-GAL4;Tub-GAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Triglyceride change Cutoff: Z-score > 1.65 after 3 screening rounds Notes: Additional information about the primary screen
Serratia marcescens infection (1)	CG12462	CG12462	7025	-1.9	none	no
Reference Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al., 2009 Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity. View Phenotypes Download PubMed Screen details Stable Id: GR00142-A-1 Screen title: Serratia marcescens infection (1) Assay: Heat shock and viability Method: Fly count Scope: Random genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: HSP70-GAL4; TubGAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Days life time (LT50) Cutoff: < -1.5 SD OR > 2 SD Notes:
Serratia marcescens infection (1)	CG12462	CG12462	7025	-2.45	none	no
Reference Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al., 2009 Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity. View Phenotypes Download PubMed Screen details Stable Id: GR00142-A-1 Screen title: Serratia marcescens infection (1) Assay: Heat shock and viability Method: Fly count Scope: Random genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: HSP70-GAL4; TubGAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Days life time (LT50) Cutoff: < -1.5 SD OR > 2 SD Notes:
Heat nociception (1)	CG2829	tlk	20905	-1.17	none	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Cell size and cell-cycle regulation (1)	FBgn0011571\|FBgn0052782	caz\|CG32782	GM09207	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Mitosis	FBgn0086899	CG32782	np	np	Dim gamma-tubulin (centrosome)	no
Reference Genes required for mitotic spindle assembly in Drosophila S2 cells. Goshima et al., 2007 The formation of a metaphase spindle, a bipolar microtubule array with centrally aligned chromosomes, is a prerequisite for the faithful segregation of a cell''s genetic material. Using a full-genome RNA interference screen of Drosophila S2 cells, we identified about 200 genes that contribute to spindle assembly, more than half of which were unexpected. The screen, in combination with a variety of secondary assays, led to new insights into how spindle microtubules are generated; how centrosomes are positioned; and how centrioles, centrosomes, and kinetochores are assembled. View Phenotypes Download PubMed Screen details Stable Id: GR00073-A-0 Screen title: Mitosis Assay: Mitotic Spindle Assembly Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , OpenBiosystems Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Lipid storage	FBgn0026698		DRSC22924	-4.16	Lipid understorage	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Innate immunity	FBgn0086899	tlk	np	np	Increased IMD reporter activity	no
Reference Inhibitor of apoptosis 2 and TAK1-binding protein are components of the Drosophila Imd pathway. Kleino et al., 2005 The Imd signaling cascade, similar to the mammalian TNF-receptor pathway, controls antimicrobial peptide expression in Drosophila. We performed a large-scale RNAi screen to identify novel components of the Imd pathway in Drosophila S2 cells. In all, 6713 dsRNAs from an S2 cell-derived cDNA library were analyzed for their effect on Attacin promoter activity in response to Escherichia coli. We identified seven gene products required for the Attacin response in vitro, including two novel Imd pathway components: inhibitor of apoptosis 2 (Iap2) and transforming growth factor-activated kinase 1 (TAK1)-binding protein (TAB). Iap2 is required for antimicrobial peptide response also by the fat body in vivo. Both these factors function downstream of Imd. Neither TAB nor Iap2 is required for Relish cleavage, but may be involved in Relish nuclear localization in vitro, suggesting a novel mode of regulation of the Imd pathway. Our results show that an RNAi-based approach is suitable to identify genes in conserved signaling cascades. View Phenotypes Download PubMed Screen details Stable Id: GR00043-A-0 Screen title: Innate immunity Assay: IMD/Rel signaling Method: Dual luciferase Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , Custom-made Reagent type: dsRNA Score type: Percentage IMD reporter activity Cutoff: >= 300% Notes:
Cell size and cell-cycle regulation (1)	FBgn0028489	CG2829	CT9660	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0010228\|FBgn0052782	HmgZ\|CG32782	LD14406	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0052782	CG32782	GM01028	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0036172\|FBgn0052782	Mob1\|CG32782	np	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0036172\|FBgn0052782	Mob1\|CG32782	GH13236	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0038223\|FBgn0052782	CG8538\|CG32782	HL04319	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Heat nociception (1)	CG12462	tlk	7026	-0.26	Lethal	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Cell size and cell-cycle regulation (1)	FBgn0024308\|FBgn0052782	Smr\|CG32782	GH07910	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Notch induced transcription	CG32782	tlk	np	-3.69	Downregulation of Notch pathway after Notch stimulation	yes
Reference Modifiers of notch transcriptional activity identified by genome-wide RNAi. Mourikis et al., 2010 The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. View Phenotypes Download PubMed Screen details Stable Id: GR00152-A Screen title: Notch induced transcription Assay: Notch pathway reporter Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: DRSC, np Reagent type: dsRNA Score type: Z-score Cutoff: < -2 OR > 2 (con-luc) OR < -1.8 OR > 1.8 (m3-luc) Notes: Additional information about secondary screens
Actin organization and cell morphology (4)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	none	yes
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-4 Screen title: Actin organization and cell morphology (4) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: BG2-c2 Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Serratia marcescens infection (1)	CG32782	CG32782	46425	1.16	none	no
Reference Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al., 2009 Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity. View Phenotypes Download PubMed Screen details Stable Id: GR00142-A-1 Screen title: Serratia marcescens infection (1) Assay: Heat shock and viability Method: Fly count Scope: Random genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: HSP70-GAL4; TubGAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Days life time (LT50) Cutoff: < -1.5 SD OR > 2 SD Notes:
Notch pathway regulation (4)	CG34412		46425	0	none	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Cell cycle	FBgn0086899	tlk	np	np	Cell cycle disfunction	no
Reference Genome-wide survey of protein kinases required for cell cycle progression. Bettencourt-Dias et al., 2004 Cycles of protein phosphorylation are fundamental in regulating the progression of the eukaryotic cell through its division cycle. Here we test the complement of Drosophila protein kinases (kinome) for cell cycle functions after gene silencing by RNA-mediated interference. We observed cell cycle dysfunction upon downregulation of 80 out of 228 protein kinases, including most kinases that are known to regulate the division cycle. We find new enzymes with cell cycle functions; some of these have family members already known to phosphorylate microtubules, actin or their associated proteins. Additionally, depletion of several signalling kinases leads to specific mitotic aberrations, suggesting novel roles for familiar enzymes. The survey reveals the inter-digitation of systems that monitor cellular physiology, cell size, cellular stress and signalling processes with the basic cell cycle regulatory machinery. View Phenotypes Download PubMed Screen details Stable Id: GR00030-A-0 Screen title: Cell cycle Assay: Cell cycle Method: FACS / High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , Custom-made Reagent type: dsRNA Score type: FACS / Visual inspection Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0052781\|FBgn0030758	CanA-14F\|CG32781	RE14919	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Drosophila small RNA pathways		tlk	DRSC22926	0.66	siRNA reporter downregulated	no
Reference Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Zhou et al., 2008 The specificity of RNAi pathways is determined by several classes of small RNAs, which include siRNAs, piRNAs, endo-siRNAs, and microRNAs (miRNAs). These small RNAs are invariably incorporated into large Argonaute (Ago)-containing effector complexes known as RNA-induced silencing complexes (RISCs), which they guide to silencing targets. Both genetic and biochemical strategies have yielded conserved molecular components of small RNA biogenesis and effector machineries. However, given the complexity of these pathways, there are likely to be additional components and regulators that remain to be uncovered. We have undertaken a comparative and comprehensive RNAi screen to identify genes that impact three major Ago-dependent small RNA pathways that operate in Drosophila S2 cells. We identify subsets of candidates that act positively or negatively in siRNA, endo-siRNA, and miRNA pathways. Our studies indicate that many components are shared among all three Argonaute-dependent silencing pathways, though each is also impacted by discrete sets of genes. View Phenotypes Download PubMed Screen details Stable Id: GR00004-A-0 Screen title: Drosophila small RNA pathways Assay: miRNA and siRNA pathway activity Method: Dual luciferase Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: , DRSC Reagent type: dsRNA Score type: Fold change endo-siRNA reporter Cutoff: 1.5/0.6 Notes:
Cell size and cell-cycle regulation (1)	FBgn0051249\|FBgn0052782	CG31249\|CG32782	RE44040	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Dpp pathway regulation		tlk	DRSC22926	weak	Decreased Flag-Mad nuclear accumulation	no
Reference Msk is required for nuclear import of TGF-{beta}/BMP-activated Smads. Xu et al., 2007 Nuclear translocation of Smad proteins is a critical step in signal transduction of transforming growth factor beta (TGF-beta) and bone morphogenetic proteins (BMPs). Using nuclear accumulation of the Drosophila Smad Mothers against Decapentaplegic (Mad) as the readout, we carried out a whole-genome RNAi screening in Drosophila cells. The screen identified moleskin (msk) as important for the nuclear import of phosphorylated Mad. Genetic evidence in the developing eye imaginal discs also demonstrates the critical functions of msk in regulating phospho-Mad. Moreover, knockdown of importin 7 and 8 (Imp7 and 8), the mammalian orthologues of Msk, markedly impaired nuclear accumulation of Smad1 in response to BMP2 and of Smad2/3 in response to TGF-beta. Biochemical studies further suggest that Smads are novel nuclear import substrates of Imp7 and 8. We have thus identified new evolutionarily conserved proteins that are important in the signal transduction of TGF-beta and BMP into the nucleus. View Phenotypes Download PubMed Screen details Stable Id: GR00014-A Screen title: Dpp pathway regulation Assay: Flag-Mad protein expression and subcellular location Method: Fluorescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2R+ Library: rp, rp Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Lipid storage	FBgn0026698		DRSC22926	-0.02	Lipid understorage	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Notch pathway regulation (4)	CG34412		20905	sp	Completely lethal (before pupal)	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Serratia marcescens infection (1)	CG12462	CG12462	7025	-1.75	none	no
Reference Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al., 2009 Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity. View Phenotypes Download PubMed Screen details Stable Id: GR00142-A-1 Screen title: Serratia marcescens infection (1) Assay: Heat shock and viability Method: Fly count Scope: Random genes Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: HSP70-GAL4; TubGAL80ts Library: VDRC, np Reagent type: UAS-IR construct Score type: Days life time (LT50) Cutoff: < -1.5 SD OR > 2 SD Notes:
Constitutive protein secretion and Golgi organization (1)	FBgn0029675	CG12462	DRSC17835	sp	Decreased horseradish peroxidase protein expression	no
Reference Functional genomics reveals genes involved in protein secretion and Golgi organization. Bard et al., 2006 Yeast genetics and in vitro biochemical analysis have identified numerous genes involved in protein secretion. As compared with yeast, however, the metazoan secretory pathway is more complex and many mechanisms that regulate organization of the Golgi apparatus remain poorly characterized. We performed a genome-wide RNA-mediated interference screen in a Drosophila cell line to identify genes required for constitutive protein secretion. We then classified the genes on the basis of the effect of their depletion on organization of the Golgi membranes. Here we show that depletion of class A genes redistributes Golgi membranes into the endoplasmic reticulum, depletion of class B genes leads to Golgi fragmentation, depletion of class C genes leads to aggregation of Golgi membranes, and depletion of class D genes causes no obvious change. Of the 20 new gene products characterized so far, several localize to the Golgi membranes and the endoplasmic reticulum. View Phenotypes Download PubMed Screen details Stable Id: GR00047-A-1 Screen title: Constitutive protein secretion and Golgi organization (1) Assay: Horseradish peroxidase protein expression Method: Luminescence Scope: Genome-wide Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DRSC Reagent type: dsRNA Score type: Z-score Cutoff: < -1.5 Notes:
Cell size and cell-cycle regulation (1)	FBgn0039570\|FBgn0052782	CG32782\|CG12870	LD29955	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Actin organization and cell morphology (2)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	Altered cell morphology	yes
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-2 Screen title: Actin organization and cell morphology (2) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2R+ Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0037346\|FBgn0052782	eIF-5C\|CG32782	SD01122	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Cell size and cell-cycle regulation (1)	FBgn0028489	CG2829	np	sp	Increased G2 DNA content	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
Heat nociception (1)	CG12462	Smr	7026	-0.26	Lethal	yes
Reference A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al., 2010 Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing. View Phenotypes Download PubMed Screen details Stable Id: GR00135-A-1 Screen title: Heat nociception (1) Assay: Noxious heat avoidance and viability Method: Fly count Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Organism Biomodel: elav-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Z-score Cutoff: > 1.65 Notes: Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
Actin organization and cell morphology (6)	FBgn0026698	tlk	CG2829 (Baum_Lab) CG32782 (UCSF)	np	Altered cell morphology	no
Reference Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology. Liu et al., 2009 In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. View Phenotypes Download PubMed Screen details Stable Id: GR00201-A-6 Screen title: Actin organization and cell morphology (6) Assay: alpha-Tubulin and F-actin protein expression Method: Fluorescence Scope: Kinases Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: BG3-c2 Library: Custom-made, Custom-made Reagent type: dsRNA Score type: Visual inspection Cutoff: np Notes:
Notch pathway regulation (4)	CG4013\|CG34412		7025	sp	Completely lethal (pupal)	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Lipid storage	FBgn0052781		DRSC23163	-1.44	none	no
Reference COPI complex is a regulator of lipid homeostasis. Beller et al., 2008 Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets. View Phenotypes Download PubMed Screen details Stable Id: GR00002-A-0 Screen title: Lipid storage Assay: Lipid droplet staining Method: High content (microscopy) Scope: Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: Kc167 Library: , DRSC Reagent type: dsRNA Score type: B-score Cutoff: 2.0 / -1.7 Notes:
Notch pathway regulation (4)	CG34412		46424	sp	Completely lethal (pupal)	no
Reference Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al., 2009 Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome. View Phenotypes Download PubMed Screen details Stable Id: GR00144-A-4 Screen title: Notch pathway regulation (4) Assay: External sensory organ morphology and viability Method: Visual inspection Scope: Genome-wide Screen type: in vivo Species: Drosophila melanogaster Biosource: Tissue Biomodel: pnr-GAL4 Library: VDRC, np Reagent type: UAS-IR construct Score type: Phenotype strength Cutoff: np Notes:
Cell size and cell-cycle regulation (1)	FBgn0052782\|FBgn0033849	CG6119\|CG32782	RH14816	sp	none	no
Reference Identification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al., 2006 Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity. View Phenotypes Download PubMed Screen details Stable Id: GR00048-A-1 Screen title: Cell size and cell-cycle regulation (1) Assay: Cell size, DNA content and viability Method: Flow cytometry Scope: Kinases, phosphatases and selected genes Screen type: Cell-based Species: Drosophila melanogaster Biosource: Cell line Biomodel: S2 Library: Custom-made, DGC1, DGC2 and PHOSPHO Reagent type: dsRNA Score type: Complex, sp Cutoff: Complex criteria Notes: Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)

Reagent information for gene 318206 (tlk)

Reagent ID	Type	Library
BKN50352	dsRNA	BKN\|Boutros Lab\|1\|FlyBase release 4, 5\|19708\|dsRNA\|http://b110-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/Drosophila+RNAi+libraries
DRSC22938	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
BKN50260	dsRNA	BKN\|Boutros Lab\|1\|FlyBase release 4, 5\|19708\|dsRNA\|http://b110-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/Drosophila+RNAi+libraries
MRC140_F03	dsRNA	MRC\|MRC\|1\|FlyBase release 2\|13089\|dsRNA\|http://www.hutchison-mrc.cam.ac.uk/
HFA17731	dsRNA	Heidelberg Fly Array (HFA)\|Boutros Lab\|1\|FlyBase release 2\|21306\|dsRNA\|http://b110-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/Drosophila+RNAi+libraries
DRSC17835	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
AMB31569	dsRNA	Ambion\|Ambion\|1\|FlyBase release 2\|13071\|dsRNA\|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
BKN28036	dsRNA	BKN\|Boutros Lab\|1\|FlyBase release 4, 5\|19708\|dsRNA\|http://b110-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/Drosophila+RNAi+libraries
DRSC37991	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
DRSC17731	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
DRSC22926	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
AMB34856	dsRNA	Ambion\|Ambion\|1\|FlyBase release 2\|13071\|dsRNA\|http://www.invitrogen.com/site/us/en/home/brands/ambion.html?CID=fl-ambion
73176	dsRNA	Open Biosystems\|Open Biosystems\|1 and 2\|FlyBase release 2 - 4\|15466\|dsRNA\|http://www.openbiosystems.com/
DRSC22924	dsRNA	DRSC\|Drosophila RNAi Screening Center (DRSC)\|2\|FlyBase release 2 - 5\|42076\|dsRNA\|http://www.flyrnai.org/
HFA17835	dsRNA	Heidelberg Fly Array (HFA)\|Boutros Lab\|1\|FlyBase release 2\|21306\|dsRNA\|http://b110-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/Drosophila+RNAi+libraries
7025	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
7026	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
105732	UAS-IR construct	KK\|Vienna Drosophila RNAi Center (VDRC)\|null\|FlyBase\|10714\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
20905	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
46423	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
46424	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
46425	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main
46426	UAS-IR construct	GD\|Vienna Drosophila RNAi Center (VDRC)\|1\|FlyBase release 3\|21066\|UAS-IR construct\|http://stockcenter.vdrc.at/control/main

Gene information for gene 318206 (tlk)

Gene:	tlk
Alternate gene names:	TLK, l(1)G0054, CG33219, CG32781, CG12462, CG32782, DmelCG34412, BcDNA:GH07910, CG34412, EP1413, EP(X)1413, dtlk, Tlk, anon-WO03040301.116, CG2829, anon-WO03040301.114
Description:	Tousled-like kinase
Chromosome:	X
Locus:
Biotype:	protein-coding
Status:	live
Entrez Gene ID:	318206
Homologs:	1
FLYBASE:	FBgn0086899
Uniprot:	Q8IRT7 Q1RL19 B7Z120 Q8IRT8 Q9W4Q4 B7Z126
RefSeq ID:	-

Homologs:

Gene	Chromosome	Locus	Organism
TLK2	17	17q23	Homo sapiens

Phenotype information for gene 318206 (tlk)

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