TITLE

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

AUTHOR(S)
Fabre, Juliette; Dauzat, Myriam; Nègre, Vincent; Wuyts, Nathalie; Tireau, Anne; Gennari, Emilie; Neveu, Pascal; Tisné, Sébastien; Massonnet, Catherine; Hummel, Irène; Granier, Christine
PUB. DATE
January 2011
SOURCE
BMC Plant Biology;2011, Vol. 11 Issue 1, p77
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Renewed interest in plant x environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community. Description: PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of Arabidopsis thaliana plant images. Conclusions: Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype x environment interactions.
ACCESSION #
62639914

 

Related Articles

  • Specific functions of individual class III peroxidase genes. Cosio, Claudia; Dunand, Christophe // Journal of Experimental Botany;Feb2009, Vol. 60 Issue 2, p391 

    In higher plants, class III peroxidases exist as large multigene families (e.g. 73 genes in Arabidopsis thaliana). The diversity of processes catalysed by peroxidases as well as the large number of their genes suggests the possibility of a functional specialization of each isoform. In addition,...

  • Natural Variation in the Degree of Autonomous Endosperm Formation Reveals Independence and Constraints of Embryo Growth During Seed Development in Arabidopsis thaliana. Ungru, Alexander; Nowack, Moritz K.; Reymond, Matthieu; Shirzadi, Reza; Kumar, Manoj; Biewers, Sandra; Grini, Paul E.; Schnittger, Arp // Genetics;Jun2008, Vol. 179 Issue 2, p829 

    Seed development in flowering plants is a paradigm for the coordination of different tissues during organ growth. It requires a tight interplay between the two typically sexually produced structures: the embryo, developing from the fertilized egg cell, and the endosperm, originating from a...

  • Mutation in LSU4 gene affects flower development in Arabidopsis thaliana. Myakushina, Yu. A.; Milyaeva, E. L.; Romanov, G. A.; Nikiforova, V. Yu. // Doklady Biochemistry & Biophysics;Oct2009, Vol. 428 Issue 1, p257 

    The article investigates the impact of LSU4 gene on the flower development in Arabidopsis thaliana plants. The main objective of the research is to determine the role of LSU4 gene in the mutation of plants. Results of the study do not show significant differences between the LSU4 mutants and...

  • Genes encoding ADP-ribosylation factors in Arabidopsis thaliana L. Heyn.; genome analysis and antisense suppression. Gebbie, Leigh K.; Burn, Joanne E.; Hocart, Charles H.; Williamson, Richard E. // Journal of Experimental Botany;Apr2005, Vol. 56 Issue 414, p1079 

    Vesicle trafficking delivers proteins to intracellular and extracellular compartments, cellulose synthase to the plasma membrane, and non-cellulosic polysaccharides to the cell wall. The Arabidopsis genome potentially encodes 19 proteins with sequence similarities to ARFs (ADP-ribosylation...

  • Evolution of Class Ill Homeodomain-Leucine Zipper Genes in Streptophytes. Floyd, Sandra K.; Zalewski, Christopher S.; Bowman, John L. // Genetics;May2006, Vol. 173 Issue 1, p373 

    Land plants underwent tremendous evolutionary change following the divergence of the ancestral lineage from algal relatives. Several important developmental innovations appeared as the embryophyte clade diversified, leading to the appearance of new organs and tissue types. To understand how...

  • In Vivo Function of Tic22, a Protein Import Component of the Intermembrane Space of Chloroplasts. Rudolf, Mareike; Machettira, Anu B.; Groß, Lucia E.; Weber, Katrin L.; Bolte, Kathrin; Bionda, Tihana; Sommer, Maik S.; Maier, Uwe G.; Weber, Andreas P.M.; Schleiff, Enrico; Tripp, Joanna // Molecular Plant (Oxford University Press / USA);May2013, Vol. 6 Issue 3, p817 

    Preprotein import into chloroplasts depends on macromolecular machineries in the outer and inner chloroplast envelope membrane (TOC and TIC). It was suggested that both machineries are interconnected by components of the intermembrane space (IMS). That is, amongst others, Tic22, of which two...

  • Characterization of rice nucleotide sugar transporters capable of transporting UDP-galactose and UDP-glucose. Seino, Junichi; Ishii, Kumiko; Nakano, Takeshi; Ishida, Nobuhiro; Tsujimoto, Masafumi; Hashimoto, Yasuhiro; Takashima, Shou // Journal of Biochemistry;Jul2010, Vol. 148 Issue 1, p35 

    Using the basic local alignment search tool (BLAST) algorithm to search the Oryza sativa (Japanese rice) nucleotide sequence databases with the Arabidopsis thaliana UDP-galactose transporter sequences as queries, we found a number of sequences encoding putative O. sativa UDP-galactose...

  • Tropaeolum Tops Tobacco – Simple and Efficient Transgene Expression in the Order Brassicales. Pitzschke, Andrea // PLoS ONE;Sep2013, Vol. 8 Issue 9, p1 

    Transient expression systems are valuable tools in molecular biology. Agrobacterial infiltration of leaves is well-established in tobacco, but has led to limited success in the model plant Arabidopsis thaliana. An efficient expression system combining the advantages of Arabidopsis...

  • The At4g11330 (ATMPK5) Locus of Arabidopsis thaliana: Updating the Annotation. Giuliani, Concetta; Heberle-Bors, Erwin; Wilson, Cathal // Plant Molecular Biology Reporter;Dec2003, Vol. 21 Issue 4, p327 

    The completed sequence of the Arabidopsis genome shows that a single base pair deletion exists in the gene encoding the MAP kinase ATMPK5 (locus At4g11330) when compared with the cDNA. This has led to the annotation of ATMPK5 in databases as a truncated protein kinase or with a deletion in...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics