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GenomeRNAi: a database for cell-based RNAi phenotypes
2007
Nucleic Acids Research
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The GenomeRNAi database (http://www .genomernai.org/) contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. ...
The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. ...
DATABASE CONTENT The updated GenomeRNAi database integrates information about RNAi reagents, their annotated targets and phenotypic information based on large-scale RNAi screens in Drosophila and human ...
doi:10.1093/nar/gkl906
pmid:17135194
pmcid:PMC1747177
fatcat:jh3cnbtopvhdjp5smd7y5axx6m
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update
2009
Nucleic Acids Research
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The GenomeRNAi database (http://www .genomernai.org/) contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. ...
The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. ...
DATABASE CONTENT The updated GenomeRNAi database integrates information about RNAi reagents, their annotated targets and phenotypic information based on large-scale RNAi screens in Drosophila and human ...
doi:10.1093/nar/gkp1038
pmid:19910367
pmcid:PMC2808900
fatcat:hhxaustndncdregg7yslsax74q
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update
2012
Nucleic Acids Research
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The GenomeRNAi database (http://www.genomernai.org) makes available RNAi phenotype data extracted from the literature for human and Drosophila. ...
RNA interference (RNAi) represents a powerful method to systematically study loss-of-function phenotypes on a large scale with a wide variety of biological assays, constituting a rich source for the assignment ...
They are grateful to Marco Breinig for critical comments on the manuscript. ...
doi:10.1093/nar/gks1170
pmid:23193271
pmcid:PMC3531141
fatcat:5dp6n47pdjcnphy73jmqtl2qgy
FlyNet: a versatile network prioritization server for theDrosophilacommunity
2015
Nucleic Acids Research
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A platform technology for predicting candidate genes or functions would further enhance the usefulness of this long-established model organism for gene-to-phenotype mapping. ...
Recently, the power of network prioritization for geneto-phenotype mapping has been demonstrated in many organisms. ...
(D) The assessment of gene prioritization for 389 RNAi phenotypes derived from the GenomeRNAi database. ...
doi:10.1093/nar/gkv453
pmid:25943544
pmcid:PMC4489278
fatcat:m6ah6bh5fbb7lkruqy3u27uodm
The FLIGHT Drosophila RNAi database
2010
Fly
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In the 'Search' section, users can search for a gene, RNAi reagent, phenotype or cell line of interest. ...
Triggering of the RNAi pathway by short double-stranded RNAs leads to the degradation of homologous mRNA within cells. 1 Thus, RNAi can elicit a loss-of-function phenotype for any gene, specified by ...
doi:10.4161/fly.4.4.13303
pmid:20855970
pmcid:PMC3174485
fatcat:xomdn3kmrzgc7nljmrpsefb4ey
The systematic identification of cytoskeletal genes required for Drosophila melanogaster muscle maintenance
2014
Scientific Data
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Using RNA interference (RNAi), we knocked down 238 genes in Drosophila and assayed for climbing ability with a robust behavioural assay. ...
Understanding the mechanisms by which tissues maintain their complex architecture is a key goal of cell biology. ...
Acknowledgements We are indebted to Dr John Petkau and Yanling Cai from the Department of Statistics, University of British Columbia, for their assistance in developing the statistical model. ...
doi:10.1038/sdata.2014.2
pmid:25977760
pmcid:PMC4365872
fatcat:jex6lewqajf2rhabuwdnxobpra
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions
2013
Nature Methods
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Here we have developed a computational framework to predict the signs (positive or negative) of physical interactions using RNAi screens. ...
Furthermore, databases of signaling pathways are incomplete, and annotations are inconsistent across databases 9 . ...
We compiled Drosophila RNAi screens that cover 49 phenotypes from the following resources: (i) Drosophila RNAi Screening Center (DRSC, http://www.flyrnai. org/), (ii) GenomeRNAi (http://genomernai.de/GenomeRNAi ...
doi:10.1038/nmeth.2733
pmid:24240319
pmcid:PMC3877743
fatcat:x5tbmczqhfgkvnifwj25z77wiq
Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster
2020
NAR Genomics and Bioinformatics
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Here, we harnessed comprehensive genomic-phenomic datasets publicly available for D. melanogaster and a machine-learning-based workflow to predict essential genes of this fly. ...
Characterizing genes that are critical for the survival of an organism (i.e. essential) is important to gain a deep understanding of the fundamental cellular and molecular mechanisms that sustain life. ...
However, these two databases do not include RNAi data from GenomeRNAi (16) or mutant allele data from FlyBase (12) . ...
doi:10.1093/nargab/lqaa051
pmid:33575603
pmcid:PMC7671374
fatcat:x5sixw7yxvae7hqt2jdtx7izpm
Cellular phenotype database: a repository for systems microscopy data
2015
Bioinformatics
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Motivation: The Cellular Phenotype Database (CPD) is a repository for data derived from highthroughput systems microscopy studies. ...
The database has a flexible structure for management of data from heterogeneous sources of systems microscopy experimental outputs generated by a variety of protocols and technologies and can be queried ...
We are also grateful to Simon Jupp and EBI Samples, Phenotypes and Ontologies Team for providing us with the mapping of the original phenotype terms to the CMPO ontology. ...
doi:10.1093/bioinformatics/btv199
pmid:25861964
pmcid:PMC4528631
fatcat:r6b2cfe5wve7finlcj7uyaotni
FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update
2011
Nucleic Acids Research
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(RNAi) screening in Drosophila cells and RNAi screen results. ...
FlyRNAi (http://www.flyrnai.org), the database and website of the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School, serves a dual role, tracking both production of reagents for RNA interference ...
DasGupta and colleagues at the NYU RNAi Core for collaboration on bioinformatically defined sub-library collections. ...
doi:10.1093/nar/gkr953
pmid:22067456
pmcid:PMC3245182
fatcat:catsyqyf4fdnnh4pq3jmf4rmpy
Knocking down the obstacles to functional genomics data sharing
2017
Scientific Data
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GenomeRNAi, initially described in 2007 by Michael Boutros and colleagues at DKFZ, was a pioneering database in this field 1 . ...
Yet, the majority of datasets have been acquired from publications and thus suffered from a lack of adequate author-provided descriptions and, at least for mammalian cell-based screens, frequently contained ...
For example, Wu et al. 9 present a valuable comparison of results from RNAi-mediated knockdown and CRISPR/Cas9-mediated knockout, and Sun et al. 8 include a comparison to transcriptomics data. ...
doi:10.1038/sdata.2017.19
pmid:28248922
pmcid:PMC5332007
fatcat:g6vrko5zorbaji7ypf27nfuodu
Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells
2015
G3: Genes, Genomes, Genetics
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To facilitate functional characterization of RBPs, we generated an RNA interference (RNAi) library for Drosophila cell-based screens comprising reagents targeting known or putative RBPs. ...
; and total ATP and image data useful for comparison of those additional assay results with fundamental information such as effects of a given reagent in the library on cell viability. ...
Kim and Mallory A. Freeberg (University of Michigan Life Sciences Institute) for their help building the RBPs gene list. ...
doi:10.1534/g3.115.019364
pmid:26199285
pmcid:PMC4555228
fatcat:qp4ejufdk5bsvp252bfqisy55m
HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects
2013
Database: The Journal of Biological Databases and Curation
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mined for phenotypic discovery. ...
It also provides a repository for additional measurements obtained from screens that were not the focus of the project, such as cell viability, and groups these data so that it can provide a gene-centric ...
Acknowledgements The authors thank their colleagues at the LRI for allowing to make their hard-won data public before publication, and Ilaria Gori and Nicholas McGranahan for helpful comments on the manuscript ...
doi:10.1093/database/bat072
pmid:24122843
pmcid:PMC3796064
fatcat:jqb6t7zjdzcq3pri6r462fyku4
Functional genomics in Drosophila models of human disease
2012
Briefings in Functional Genomics
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Whether the system is based on the over-expression of a toxic variant of a human protein or requires the loss of function of an orthologous fly gene, the consequent phenotypes can be used to understand ...
Such an observation is often sufficient justification for the creation of a disease model in the fly. ...
Recently, the online database GenomeRNAi has documented most of the genome-wide cell based and in vivo RNAi screens (http://genomernai.de/ GenomeRNAi/, [58] ). ...
doi:10.1093/bfgp/els038
pmid:22914042
fatcat:fydmoqothbfpdh3n4hxjkp4xum
RNAi screening in Drosophila cells and in vivo
2014
Methods
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Specifically, I discuss the types of high-throughput assays that can be done in Drosophila cells and in vivo, RNAi reagent design and available reagent collections, automated screen pipelines, analysis ...
of screen results, and approaches to RNAi results verification. ...
Acknowledgments I extend my thanks to Norbert Perrimon, Liz Perkins, and the DRSC/TRiP staff for many helpful discussions. ...
doi:10.1016/j.ymeth.2014.02.018
pmid:24576618
pmcid:PMC4206080
fatcat:kg3ntg2wzvdczbfjwz7zwb6ate
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