Agriculture Reference
In-Depth Information
AraCyc/PoplarCyc
AraCyc and PoplarCyc are also available at the PMN web site, which provides a
review of information about metabolic pathways in Arabidopsis and poplar respec-
tively (Mueller et al.
2003
). There are also metabolic pathway databases for several
other plant species generated by PMN researchers. MapMan is a tool to project
'omics' data onto metabolic pathways (Thimm et al.
2004
).
KaPPA-View
KaPPA-View is a web-based analysis tool that can be used to superimpose tran-
scriptome and metabolome data onto plant metabolic pathway maps (Tokimatsu
et al.
2005
).
PRIMe
PRIMe is a web-based service that provides data of metabolites measured by multi-
dimensional NMR spectroscopy, GC-MS, LC-MS and CE-MS, in an integrated ap-
proach to analysis of comprehensive data within the metabolome and transcriptome
search engines present there (Akiyama et al.
2008
).
Plant Phenotype (Phenome) Analysis
Analysis of mutants is an effective approach for investigation of gene structure and
function (Springer
2000
; Stanford et al.
2001
). Collections of mutant lines are also
essential bioresources for accelerating forward and reverse genetics in plants. The
available mutant resources for phenome analysis in plant species have been well
described in a recent review by Kuromori et al. (
2009
). The demand for compre-
hensive collection of mutants and related information has increased dramatically
encouraged by the high-throughput and genome-wide phenome analysis in plants
(Alonso and Ecker
2006
). Listed below are six of the most important web-based
sites for phenome analysis and insertion mutants, their purpose and their URL are
detailed in Table
2.11
.
InsertionMutants
Insertion mutant resources with index data that document the inserted gene muta-
tion position have become extremely beneficial resources to investigate functional
analysis of genes that can be up-regulated by promoters, or disrupted, down-regu-
lated and silenced by reverse genetics.
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