title: Plant MetGenMAP: an integrative analysis system for plant systems biology.
abstract: The information and resources generated from diverse "omics" technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP.
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA.
authors.forename: Je-Gun
authors.initials: JG
authors.lastname: Joung
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Corbett
authors.forename: Shanna Moore
authors.initials: SM
authors.lastname: Fellman
authors.forename: Denise M
authors.initials: DM
authors.lastname: Tieman
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Klee
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects; D002338:Carotenoids / Q000096:biosynthesis; D005632:Fructose / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D005947:Glucose / Q000378:metabolism; D007178:Inbreeding; D020407:Internet; D008027:Light; D018551:Solanum lycopersicum / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000528:radiation effects; D055442:Metabolome / Q000235:genetics / Q000528:radiation effects; D010641:Phenotype; D010944:Plants / Q000235:genetics* / Q000378:metabolism* / Q000528:radiation effects; D011401:Promoter Regions, Genetic / Q000235:genetics; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors
chemical_list: D005632:Fructose; D002338:Carotenoids; D005947:Glucose