Technical Abstract: We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. Plant MetGenMAP is an easy-to-use, powerful analysis system that supports many functions of systems biology analyses in the context of biochemical pathways and gene ontology (GO) terms. It provides an analytical platform in which highly altered pathways can be explored rapidly and efficiently through intuitive visualization and robust statistical tests. Since it allows for the analysis of transcriptional and metabolic changes simultaneously for each pathway, the association between gene expression and biochemical changes in specific pathways under specific conditions can be easily inferred. Functional analysis of differentially regulated pathways can help to properly define functional roles of genes within pathways. In addition, the system embeds a function that can identify major regulators putatively related to the change of transcripts and metabolites in specific pathways. We present comprehensive results identified with Plant MetGenMAP including differentially regulated metabolic pathways, functions of genes associated with pathway changes, putative regulators associated with these genes, and probabilistic associations between genes, metabolites, and phenotypes.