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FlyBase--the Drosophila database. The FlyBase Consortium

1994 Nucleic Acids Research  
FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is available from the ftp.bio.indiana.edu Gopher server.  ...  The scope of FlyBase includes: genes, alleles, aberrations, pointers to sequence data, stock lists, Drosophila workers and bibliographic references.  ...  REFERENCING FLYBASE We suggest that FlyBase be referenced as follows: FlyBase (1994 ACKNOWLEDGEMENTS FlyBase is supported by a grant from the National Institutes of Health (National Center for Human  ... 
pmid:7937045 pmcid:PMC308301 fatcat:qvf56htqfvcila7dgwgkljuehi

Exploring FlyBase Data Using QuickSearch

Steven J. Marygold, Giulia Antonazzo, Helen Attrill, Marta Costa, Madeline A. Crosby, Gilberto dos Santos, Joshua L. Goodman, L. Sian Gramates, Beverley B. Matthews, Alix J. Rey, Jim Thurmond
2016 Current Protocols in Bioinformatics  
FlyBase (flybase.org) is the primary online database of genetic, genomic and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster.  ...  The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data.  ...  Support is also provided by the Indiana Genomics Initiative and the National Science Foundation through XSEDE resources provided by Indiana University.  ... 
doi:10.1002/cpbi.19 pmid:27930807 pmcid:PMC5152691 fatcat:gak43qcvjndcphz774srcxvzkq

Phenotypic data in FlyBase

R. Drysdale
2001 Briefings in Bioinformatics  
FlyBase is an international consortium, with members at Abstract Phenotypic analysis combined with molecular genetics is a powerful tool for mapping gene function onto the genome.  ...  Rachel Drysdale has been a genetic curator with FlyBase since the project began in 1992.  ...  Acknowledgements The phenotypic data in FlyBase is curated at FlyBase-Cambridge by Gillian Millburn, Chihiro Yamada and the author.  ... 
doi:10.1093/bib/2.1.68 pmid:11465064 fatcat:rof5miilfreyndoxfaoac6iu3m

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

Helen Attrill, Kathleen Falls, Joshua L. Goodman, Gillian H. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold
2015 Nucleic Acids Research  
To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual  ...  Many publications describe sets of genes or gene products that share a common biology.  ...  ACKNOWLEDGEMENTS We wish to thank: Elspeth Bruford, Ruth Seal, Susan Tweedie and Kris Gray at the HGNC for useful dis-  ... 
doi:10.1093/nar/gkv1046 pmid:26467478 pmcid:PMC4702782 fatcat:2ljorlbf4jgkrilfxniusk6pcy

FlyBase portals to human disease research usingDrosophilamodels

Gillian H. Millburn, Madeline A. Crosby, L. Sian Gramates, Susan Tweedie
2016 Disease Models & Mechanisms  
The use of Drosophila melanogaster as a model for studying human disease is well established, reflected by the steady increase in both the number and proportion of fly papers describing human disease models  ...  To facilitate this, FlyBase has developed a dedicated tool for querying and navigating relevant data, which include mutations that model a disease and any associated interacting modifiers.  ...  We thank our FlyBase colleagues for their helpful comments on the manuscript, and also thank Helen Attrill for help in preparing the figures.  ... 
doi:10.1242/dmm.023317 pmid:26935103 pmcid:PMC4826978 fatcat:yhhupuyp4zgptd7vyw2edmzedq

FlyBase: enhancing Drosophila Gene Ontology annotations

S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland, A. Schroeder, R. Seal, H. Zhang
2009 Nucleic Acids Research  
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information.  ...  Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location.  ...  S.T. would like to thank the members of the Gene Ontology Consortium and particularly the GO Reference Genome Annotation Group for support with all aspects of GO annotation and ontology development.  ... 
doi:10.1093/nar/gkn788 pmid:18948289 pmcid:PMC2686450 fatcat:ce6tuo7gxbdfzo3sfgtxshlloy

Using FlyBase to Find Functionally Related Drosophila Genes [chapter]

Alix J. Rey, Helen Attrill, Steven J. Marygold
2018 Msphere  
This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their  ...  In addition, FlyBase provides preassembled lists of functionally related D. melanogaster genes within "Gene Group" reports.  ...  The FlyBase "Gene Group" resource was established to fill this gap, allowing users to easily access lists of functionally related D. melanogaster genes [6] .  ... 
doi:10.1007/978-1-4939-7737-6_16 pmid:29761468 pmcid:PMC5996772 fatcat:4s77pj47u5gbfmo57eaa6jefl4

Using FlyBase, a Database of Drosophila Genes and Genomes [chapter]

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman
2016 Msphere  
For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster.  ...  ; other integrated reports have been established that bring together related genes, datasets or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional  ...  Gene model annotations in FlyBase For D. melanogaster, FlyBase has produced manually annotated gene models for over a decade (34) .  ... 
doi:10.1007/978-1-4939-6371-3_1 pmid:27730573 pmcid:PMC5107610 fatcat:gbtsjk6xj5esbp6wt6ttdswhp4

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, Ernst Hafen
2009 BMC Bioinformatics  
Acknowledgements The FlyBase Consortium comprises: FlyBase-Harvard: W.  ...  Such identification is not intended to imply recommendation or endorsement by the NIST, nor it is intended to imply that the materials or equipment identified are necessarily the best available for this  ...  Conclusion In this work, we established the Drosophila melanogaster PeptideAtlas, a resource of observed mass spectra matching to 76'724 fly peptides and we show it use and potentials.  ... 
doi:10.1186/1471-2105-10-59 pmid:19210778 pmcid:PMC2648944 fatcat:rg3tbhynp5g67jobpaigyd3w4e

MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion

M. Sardiello
2003 Nucleic Acids Research  
Aim of the MitoDrome database is to annotate the Drosophila melanogaster nuclear genes coding for mitochondrial proteins in order to contribute to the functional characterization of nuclear genes coding  ...  Indeed D. melanogaster is one of the most studied organisms and a model for the Human genome.  ...  The fruit fly, Drosophila melanogaster, database (FlyBase), is the official resource where data derived from literature and value-added data derived from in silico analysis are annotated.  ... 
doi:10.1093/nar/gkg123 pmid:12520013 pmcid:PMC165570 fatcat:kexspmimr5hz7atlo4v7qybioq

Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group

Rebekah L. Rogers, Ling Shao, Jaleal S. Sanjak, Peter Andolfatto, Kevin R. Thornton
2014 G3: Genes, Genomes, Genetics  
Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include UTRs and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy  ...  We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and  ...  ACKNOWLEDGMENTS We thank Rahul Warrior for offering incubator space for fly cultures and Rachel Martin for an emergency supply of liquid nitrogen.  ... 
doi:10.1534/g3.114.013532 pmid:25273863 pmcid:PMC4267930 fatcat:gbdgbyfucjhgllea5owpl2enca

OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster

Alistair Miles, Jun Zhao, Graham Klyne, Helen White-Cooper, David Shotton
2010 Journal of Biomedical Informatics  
For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection  ...  FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com.  ...  this gene in different Drosophila melanogaster body tissues.  ... 
doi:10.1016/j.jbi.2010.04.004 pmid:20382263 fatcat:axpgbbkw3zauzkajc3h3jogiga

Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome

Andrew E. Christie, Tiana M. Fontanilla, Katherine T. Nesbit, Petra H. Lenz
2013 Comparative Biochemistry and Physiology - Part D:Genomics and Proteomics  
To begin to address this possibility, we used the well-established Drosophila melanogaster circadian system as a reference for mining clock transcripts from a 200,000+ sequence Calanus transcriptome; the  ...  Recent studies in insects suggest that some circadian genes/proteins also contribute to the establishment of seasonal diapause.  ...  This resource has allowed for the mining of transcripts that encode proteins putatively involved in the establishment of a circadian clock in this ecologically critical species.  ... 
doi:10.1016/j.cbd.2013.04.002 pmid:23727418 pmcid:PMC3755088 fatcat:ldbjnklslnaq5iljneupclydzi

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

Ulrike Pfreundt, Daniel P. James, Susan Tweedie, Derek Wilson, Sarah A. Teichmann, Boris Adryan
2009 Nucleic Acids Research  
FlyTF (http://www.flytf.org) is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster.  ...  While our GO annotations will also be available through FlyBase as they will be incorporated into the genes' official GO annotation in the future, the entire evidence used for classification including  ...  ACKNOWLEDGEMENTS The authors thank Nick Brown and Steven Marygold at FlyBase for enabling UP to participate in this collaboration and for comments on the manuscript.  ... 
doi:10.1093/nar/gkp910 pmid:19884132 pmcid:PMC2808907 fatcat:mpgt6a2cuzfq3agikptnae6q6y

Drosophila melanogaster: A case study of a model genomic sequence and its consequences

M. Ashburner
2005 Genome Research  
We thank Hamid Bolouri for showing us the potential of Cytoscape. We apologize for any oversight in attribution resulting from space limitations.  ...  C.M.B. is supported by a USA Research Fellowship from the Royal Society. Work in M.A.'s laboratory is supported by an MRC Programme Grant to M.A. and Steve Russell.  ...  Figure 1 . 1 Partial gene regulatory network (GRN) for Drosophila melanogaster automatically generated from genome annotations.  ... 
doi:10.1101/gr.3726705 pmid:16339363 fatcat:ejs2jxhp7nhkfhmfk6kwpv7m24
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