OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize
-
Published:2012-12
Issue:1
Volume:12
Page:
-
ISSN:1471-2229
-
Container-title:BMC Plant Biology
-
language:en
-
Short-container-title:BMC Plant Biol
Author:
Colmsee Christian,Mascher Martin,Czauderna Tobias,Hartmann Anja,Schlüter Urte,Zellerhoff Nina,Schmitz Jessica,Bräutigam Andrea,Pick Thea R,Alter Philipp,Gahrtz Manfred,Witt Sandra,Fernie Alisdair R,Börnke Frederik,Fahnenstich Holger,Bucher Marcel,Dresselhaus Thomas,Weber Andreas PM,Schreiber Falk,Scholz Uwe,Sonnewald Uwe
Abstract
Abstract
Background
Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource for bioenergy. When looking at the problems of limited fossil fuels, the growth of the world’s population or the world’s climate change, it is important to find ways to increase the yield and biomass of maize and to study how it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology project maize plants were grown under a large set of controlled stress conditions, phenotypically characterised and plant material was harvested to analyse the effect of specific environmental conditions or developmental stages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plant material allowing the comparison of results across different omics domains. A data warehouse was developed to store experimental data as well as analysis results of the performed experiments.
Description
The OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe the functions of the selected unigenes. Several treatment- and plant growth stage experiments were performed and measured data were filled into data templates and imported into the data warehouse by a Java based import tool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is provided.
Conclusions
With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different data domains, comprises several analysis results that will support researchers within their work and supports systems biological research in particular. The system is available at http://www.optimas-bioenergy.org/optimas_dw.
Publisher
Springer Science and Business Media LLC
Reference24 articles.
1. Lawrence C, Dong Q, Polacco M, Seigfried T, Brendel V: MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res. 2004, 32: D393-D397. 10.1093/nar/gkh011. 2. Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, et al: Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res. 2006, 34: D752-D757. 10.1093/nar/gkj011. 3. Kuenne C, Grosse I, Matthies I, Scholz U, Sretenovic-Rajicic T, Stein N, Stephanik A, Steuernagel B, Weise S: Using data warehouse technology in crop plant bioinformatics. J Integr Bioinf. 2007, 4: 88. 4. Junker BH, Klukas C, Schreiber F: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinf. 2006, 7: e109-10.1186/1471-2105-7-109. 5. Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B, Klapperstück M, Scholz U, Weise S: MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 2012, 40: D1173-D1177. 10.1093/nar/gkr1004.
Cited by
46 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|