The FLIGHT Drosophila RNAi database

FLIGHT (http://flight.icr.ac.uk/) is an online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and data-mining in Drosophila.

[1]  Thomas Horn,et al.  GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update , 2009, Nucleic Acids Res..

[2]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[3]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[4]  A. von Haeseler,et al.  Genome-Wide RNAi Screen Identifies Genes Involved in Intestinal Pathogenic Bacterial Infection , 2009, Science.

[5]  Doris Chen,et al.  Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi , 2009, Nature.

[6]  David Osumi-Sutherland,et al.  FlyBase: enhancing Drosophila Gene Ontology annotations , 2008, Nucleic Acids Res..

[7]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[8]  Tao Liu,et al.  Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology , 2009, Genome Biology.

[9]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[10]  K. Dolinski,et al.  The BioGRID Interaction Database: 2008 update , 2007, Nucleic Acids Res..

[11]  Norbert Perrimon,et al.  Matter Arising: Off-Targets and Genome-Scale RNAi Screens in Drosophila , 2007, Fly.

[12]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[13]  Thomas Horn,et al.  GenomeRNAi: a database for cell-based RNAi phenotypes , 2006, Nucleic Acids Res..

[14]  Gopal R. Gopinath,et al.  Reactome: a knowledge base of biologic pathways and processes , 2007, Genome Biology.

[15]  Nir Hacohen,et al.  Minimizing the risk of reporting false positives in large-scale RNAi screens , 2006, Nature Methods.

[16]  Pengyu Hong,et al.  Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays , 2006, Nature Methods.

[17]  Lawrence Lum,et al.  Prevalence of off-target effects in Drosophila RNA interference screens , 2006, Nature.

[18]  Wolfgang Huber,et al.  Analysis of cell-based RNAi screens , 2006, Genome Biology.

[19]  David Sims,et al.  FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets , 2005, Nucleic Acids Res..

[20]  Norbert Perrimon,et al.  FlyRNAi: the Drosophila RNAi screening center database , 2005, Nucleic Acids Res..

[21]  Jaime Prilusky,et al.  SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment , 2005, Nucleic Acids Res..

[22]  A. Coulson,et al.  Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans , 2005, Nature.

[23]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[24]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[25]  N. Perrimon,et al.  Genome-Wide RNAi Analysis of Growth and Viability in Drosophila Cells , 2004, Science.

[26]  B. Baum,et al.  Abi, Sra1, and Kette Control the Stability and Localization of SCAR/WAVE to Regulate the Formation of Actin-Based Protrusions , 2003, Current Biology.

[27]  A. Coulson,et al.  A functional genomic analysis of cell morphology using RNA interference , 2003, Journal of biology.

[28]  F. Piano,et al.  Gene Clustering Based on RNAi Phenotypes of Ovary-Enriched Genes in C. elegans , 2002, Current Biology.

[29]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[30]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[31]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[32]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.