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FLAGdb++: a database for the functional analysis of the Arabidopsis genome

F. Samson
2004 Nucleic Acids Research  
FLAGdb ++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis.  ...  FLAGdb ++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and speci®cities having an impact upon the con-®dence we will put in the  ...  ACKNOWLEDGEMENTS The authors are grateful to collaborators for producing the biological data or computer predictions integrated into FLAGdb ++  ... 
doi:10.1093/nar/gkh134 pmid:14681431 pmcid:PMC308868 fatcat:63ovrr3txrbbzmrufoezjp554e

Exploration of plant genomes in the FLAGdb++ environment

Sandra Dèrozier, Franck Samson, Jean-Philippe Tamby, Cécile Guichard, Véronique Brunaud, Philippe Grevet, Séverine Gagnot, Philippe Label, Jean-Charles Leplé, Alain Lecharny, Sébastien Aubourg
2011 Plant Methods  
Conclusion: Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb ++ presents a powerful complementary tool for exploring plant  ...  In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern.  ...  The development of FLAGdb ++ has been supported in part by ANR and Génoplante projects.  ... 
doi:10.1186/1746-4811-7-8 pmid:21447150 pmcid:PMC3073958 fatcat:ou5iw7mktzf4popielzchrcvqa

GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions

Y. Li, M. G. Rosso, P. Viehoever, B. Weisshaar
2007 Nucleic Acids Research  
A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests.  ...  Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana.  ...  at MPI for Plant Breeding Research and the Chair of Genome Research at Bielefeld University for sequencing.  ... 
doi:10.1093/nar/gkl753 pmid:17062622 pmcid:PMC1781121 fatcat:awjipf4tujd5lossgxdh34x5sq

Site Preferences of Insertional Mutagenesis Agents in Arabidopsis

X. Pan
2005 Plant Physiology  
We have performed a comparative analysis of the insertion sites of engineered Arabidopsis (Arabidopsis thaliana) insertional mutagenesis vectors that are based on the maize (Zea mays) transposable elements  ...  The transposon-based agents show a bias toward insertions near the translation start codons of genes, while the T-DNAs show a predilection for the putative transcriptional regulatory regions of genes.  ...  Research, Germany, the FLAGdb/FST, France, and the Institute of Molecular Agrobiology, Singapore for allowing us to use their insertional mutagenesis data.  ... 
doi:10.1104/pp.104.053215 pmid:15618417 pmcid:PMC548848 fatcat:t25hl3wwmbgefktjvsnf2y6754

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome

Sébastien Aubourg, Marie-Laure Martin-Magniette, Véronique Brunaud, Ludivine Taconnat, Frédérique Bitton, Sandrine Balzergue, Pauline E Jullien, Mathieu Ingouff, Vincent Thareau, Thomas Schiex, Alain Lecharny, Jean-Pierre Renou
2007 BMC Genomics  
We acknowledge Franck Samson for FLAGdb ++ developments, Carine Serizet for the Eugene v1.59 annotation of the Arabidopsis genome, and Joan Sobota for correcting the manuscript.  ...  Acknowledgements We are grateful to all the CATMA partners and collaborators for the making of the micro-arrays and all the transcriptome projects used in the study.  ...  FLAGdb ++ also contains TAIR gene annota-tions, available transcript sequences and the latest version of the Eugene predictions (v1.59) for the Arabidopsis genome.  ... 
doi:10.1186/1471-2164-8-401 pmid:17980019 pmcid:PMC2174955 fatcat:x4hh3z4y7jhi3akdalhy2bcgbe

Page 935 of Cellular and Molecular Life Sciences Vol. 60, Issue 5 [page]

2003 Cellular and Molecular Life Sciences  
Bot. 52: 1593-1601 Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.  ...  ., Pelletier G. et al. (2002) FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.  ... 

GenoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

D. Samson
2003 Nucleic Acids Research  
The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis  ...  programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice).  ...  We are very grateful to our Génoplante colleagues for the submission of their data and/or tools to GPI, their participation in many bioinformatics meetings and task forces, and for their help in defining  ... 
doi:10.1093/nar/gkg060 pmid:12519976 pmcid:PMC165507 fatcat:2rggwjp6xbh3re6whcjibiblea

Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions

Yong Li, Mario G. Rosso, Bekir Ülker, Bernd Weisshaar
2006 Genomics  
Large collections of sequence-indexed T-DNA insertion mutants are invaluable resources for plant functional genomics.  ...  Flanking sequence tag (FST) data from these collections indicated that T-DNA insertions are not randomly distributed in the Arabidopsis thaliana genome and that there are still a fairly high number of  ...  This work was supported by the BMBF in the context of the German plant genomics program GABI (Förderkennzeichen 0312273).  ... 
doi:10.1016/j.ygeno.2005.12.010 pmid:16488113 fatcat:hnig3bxqsrap7ec3izncxp6via

CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform

S. Gagnot, J.-P. Tamby, M.-L. Martin-Magniette, F. Bitton, L. Taconnat, S. Balzergue, S. Aubourg, J.-P. Renou, A. Lecharny, V. Brunaud
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would like to thank Franck Samson for his help during the optimization of the code and Philippe Grevet for assistance and management of the ftp and web servers.  ...  Funding to pay the Open Access publication charges for this article was provided by INRA. The URGV CATMA resource has been funded by Ge´noplante.  ...  Database (SMD) (4, 5) and (iii) specific databases dedicated to a species like The Arabidopsis Information Resource, or the expression browser (eFP) from the Bio-Array Resource for Arabidopsis Functional  ... 
doi:10.1093/nar/gkm757 pmid:17940091 pmcid:PMC2238931 fatcat:2lh3ut2s2baido5ifdszhkatje

ATIDB: Arabidopsis thaliana insertion database

X. Pan
2003 Nucleic Acids Research  
Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function.  ...  Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions.  ...  at Cold Spring Harbor Laboratory, NY, for part of the insertion data.  ... 
doi:10.1093/nar/gkg222 pmid:12582244 pmcid:PMC150240 fatcat:gzv6zm6vybbylaioj5e77kjw7u

Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants

T. Kuromori, S. Takahashi, Y. Kondou, K. Shinozaki, M. Matsui
2009 Plant and Cell Physiology  
Acknowledgments The authors are grateful to Drs.  ...  Hirohiko Hirochika, Hiroaki Ichikawa, Takanari Ichikawa, Hiroshi Takatsuji, Masaki Mori, Kenji Oda, Hidetaka Kaya, Tetsuya Sakurai, Masanori Tamaoki and Takashi Hirayama for their valuable suggestions  ...  As a result, a large number of T-DNA or transposon-insertional lines have already been prepared for functional genomics in Arabidopsis.  ... 
doi:10.1093/pcp/pcp078 pmid:19502383 pmcid:PMC2709550 fatcat:pcorqrag7jgmppgdftxqx3wece

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

S. Aubourg
2004 Nucleic Acids Research  
The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database  ...  Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function.  ...  ACKNOWLEDGEMENTS The authors are grateful to Vincent Thareau for his help in the comparison between the GeneFarm and TIGR annotations. The GeneFarm database has been filed at the 'Agence pour la  ... 
doi:10.1093/nar/gki115 pmid:15608279 pmcid:PMC540069 fatcat:5i6iv33sffhmdgzsbedb2ggtpa

Transgenic Plants as Gene-Discovery Tools [chapter]

Yingying Meng, Hongyu Li, Tao Zhao, Chunyu Zhang, Chentao Lin, Bin Liu
2012 Transgenic Plants - Advances and Limitations  
Loss-of-function mutations The most conventional tool for the functional analysis of all genes in a certain organism is to generate indexed loss-of-function mutagenesis on a whole genome scale.  ...  functions at a genome wide level.  ...  Transgenic Plants -Advances and Limitations Development of efficient transformation protocols is becoming a complementary strategy to conventional breeding techniques for the improvement of crops.  ... 
doi:10.5772/33895 fatcat:q257532djbeixbf255usafill4

An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches

Stephen J Robinson, Lily H Tang, Brent AG Mooney, Sheldon J McKay, Wayne E Clarke, Matthew G Links, Steven Karcz, Sharon Regan, Yun-Yun Wu, Margaret Y Gruber, Dejun Cui, Min Yu (+1 others)
2009 BMC Plant Biology  
Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes.  ...  Arabidopsis genome sequence  ...  Acknowledgements The work described was supported by funding from AAFC Canadian Crop Genomics Initiative grants to IAPP and MYG, in addition YYW was partially supported by an NSERC discovery grant to SR  ... 
doi:10.1186/1471-2229-9-101 pmid:19646253 pmcid:PMC3091532 fatcat:3mzd2mkrt5envhxvugse4prfxe

OryGenesDB: a database for rice reverse genetics

G. Droc
2006 Nucleic Acids Research  
Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics.  ...  As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.  ...  We acknowledge the support of the EU 5th framework project QLG2-CT-2001-01453 CerealGene Tags and of the Generation Challenge Program.  ... 
doi:10.1093/nar/gkj012 pmid:16381969 pmcid:PMC1347375 fatcat:mxpilrarl5am5i4gf42whsvhky
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