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GenomeRNAi: a database for cell-based RNAi phenotypes

T. Horn, Z. Arziman, J. Berger, M. Boutros
2007 Nucleic Acids Research  
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

Moritz Gilsdorf, Thomas Horn, Zeynep Arziman, Oliver Pelz, Evgeny Kiner, Michael Boutros
2009 Nucleic Acids Research  
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

Esther E. Schmidt, Oliver Pelz, Svetlana Buhlmann, Grainne Kerr, Thomas Horn, Michael Boutros
2012 Nucleic Acids Research  
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

Junha Shin, Sunmo Yang, Eiru Kim, Chan Yeong Kim, Hongseok Shim, Ara Cho, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, Insuk Lee
2015 Nucleic Acids Research  
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

David Sims, Borisas Bursteinas, Ekta Jain, Qiong Gao, Buzz Baum, Marketa Zvelebil
2010 Fly  
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

Alexander D Perkins, Michael J J Lee, Guy Tanentzapf
2014 Scientific Data  
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

Arunachalam Vinayagam, Jonathan Zirin, Charles Roesel, Yanhui Hu, Bahar Yilmazel, Anastasia A Samsonova, Ralph A Neumüller, Stephanie E Mohr, Norbert Perrimon
2013 Nature Methods  
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

Tulio L Campos, Pasi K Korhonen, Andreas Hofmann, Robin B Gasser, Neil D Young
2020 NAR Genomics and Bioinformatics  
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

Catherine Kirsanova, Alvis Brazma, Gabriella Rustici, Ugis Sarkans
2015 Bioinformatics  
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

I. T. Flockhart, M. Booker, Y. Hu, B. McElvany, Q. Gilly, B. Mathey-Prevot, N. Perrimon, S. E. Mohr
2011 Nucleic Acids Research  
(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

Kaylene J. Simpson, Jennifer A. Smith
2017 Scientific Data  
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

Stephanie E. Mohr, Yanhui Hu, Kirstin Rudd, Michael Buckner, Quentin Gilly, Blake Foster, Katarzyna Sierzputowska, Aram Comjean, Bing Ye, Norbert Perrimon
2015 G3: Genes, Genomes, Genetics  
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

Rebecca E. Saunders, Rachael Instrell, Rossella Rispoli, Ming Jiang, Michael Howell
2013 Database: The Journal of Biological Databases and Curation  
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

K.-F. Chen, D. C. Crowther
2012 Briefings in Functional Genomics  
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

Stephanie E. Mohr
2014 Methods  
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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