KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data

Sakurai, Nozomu; Ara, Takeshi; Ogata, Yasuhiro; Sano, Ryosuke; Ohno, Takashi; Sugiyama, Kenjiro; Hiruta, Atsushi; Yamazaki, Kiyoshi; Yano, Kentarô; Aoki, Koh; Aharoni, Asaph; Hamada, Kazuki; Yokoyama, Koji; Kawamura, Shingo; Otsuka, Hiroyuki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Suzuki, Hideyuki; Saito, Kazuki; Shibata, Daisuke

doi:10.1093/nar/gkq989

Cited by 67 publications

(39 citation statements)

References 31 publications

(40 reference statements)

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“…The MapMan tool (Thimm et al, 2004; http://mapman.gabipd.org/ web/guest) was used to visualize the gene expression data set in the context of metabolic pathways or other processes represented in modules (bins) and to build the Venn diagrams for up-and down-regulated genes. In addition, we performed pathway analysis and interpretation of omics data using the free databases KaPPA-View4 (Tokimatsu et al, 2005;Sakurai et al, 2011; http:// kpv.kazusa.or.jp/) and the KEGG database (Kanehisa and Goto, 2000; http:// www.genome.jp/kegg/). Gene subcellular localizations and expression were searched with the ePlant server (https://bar.utoronto.ca/eplant/; University of Toronto).…”

Section: Gene Expression Data Evaluation and Pathway Analysesmentioning

confidence: 99%

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

et al. 2016

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Plants have evolved adaptive mechanisms that allow them to tolerate a continuous range of abiotic and biotic stressors. Tropospheric ozone (O 3 ), a global anthropogenic pollutant, directly affects living organisms and ecosystems, including plant-herbivore interactions. In this study, we investigate the stress responses of Brassica nigra (wild black mustard) exposed consecutively to O 3 and the specialist herbivore Pieris brassicae. Transcriptomics and metabolomics data were evaluated using multivariate, correlation, and network analyses for the O 3 and herbivory responses. O 3 stress symptoms resembled those of senescence and phosphate starvation, while a sequential shift from O 3 to herbivory induced characteristic plant defense responses, including a decrease in central metabolism, induction of the jasmonic acid/ethylene pathways, and emission of volatiles. Omics network and pathway analyses predicted a link between glycerol and central energy metabolism that influences the osmotic stress response and stomatal closure. Further physiological measurements confirmed that while O 3 stress inhibited photosynthesis and carbon assimilation, sequential herbivory counteracted the initial responses induced by O 3 , resulting in a phenotype similar to that observed after herbivory alone. This study clarifies the consequences of multiple stress interactions on a plant metabolic system and also illustrates how omics data can be integrated to generate new hypotheses in ecology and plant physiology.

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Section: Gene Expression Data Evaluation and Pathway Analysesmentioning

confidence: 99%

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

et al. 2016

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“…The transcriptome and metabolome data were integrated and applied to a metabolic pathway map using the KaPPA-View 4 KEGG system (Sakurai et al, 2011). GENESCOPE released the V0 grape genome data in 2007 (Jaillon et al, 2007), and the V0 data were registered as reference sequences in NCBI.…”

Section: Update Of the Metabolic Pathway Map Of Grape In Kegg And Thementioning

confidence: 99%

“…Principal component analysis (PCA) revealed the induction of a single metabolite by UV-C irradiation. Data from the transcriptome and metabolome analyses were projected on a metabolic map using the KaPPA-View 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) system (http://kpv.kazusa.or.jp/ kpv4-kegg-1402/; Sakurai et al, 2011) after modification to apply the whole grape gene expression. The map demonstrated the induction of the stilbene synthetic pathway by UV-C irradiation.…”

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confidence: 99%

Multiomics in Grape Berry Skin Revealed Specific Induction of the Stilbene Synthetic Pathway by Ultraviolet-C Irradiation

et al. 2015

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Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies.

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“…Additional work is needed to evaluate the conservation of differential coexpression patterns among species, and more efficient tools for their assessment in plants would be helpful. For example, like Kappa-view 4 (Sakurai et al, 2011), the mapping of differential coexpressions onto metabolic pathways is highly useful in the field of plant research. We offer our extensive analysis of the coexpression networks to aid researchers in the selection and prioritization of candidate genes in studies on tomato functional genomics.…”

Section: Discussionmentioning

confidence: 99%

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

Fukushima

Nishizawa²,

Hayakumo³

et al. 2012

Plant Physiology

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Gene-to-gene coexpression analysis provides fundamental information and is a promising approach for predicting unknown gene functions in plants. We investigated various associations in the gene expression of tomato (Solanum lycopersicum) to predict unknown gene functions in an unbiased manner. We obtained more than 300 microarrays from publicly available databases and our own hybridizations, and here, we present tomato coexpression networks and coexpression modules. The topological characteristics of the networks were highly heterogenous. We extracted 465 total coexpression modules from the data set by graph clustering, which allows users to divide a graph effectively into a set of clusters. Of these, 88% were assigned systematically by Gene Ontology terms. Our approaches revealed functional modules in the tomato transcriptome data; the predominant functions of coexpression modules were biologically relevant. We also investigated differential coexpression among data sets consisting of leaf, fruit, and root samples to gain further insights into the tomato transcriptome. We now demonstrate that (1) duplicated genes, as well as metabolic genes, exhibit a small but significant number of differential coexpressions, and (2) a reversal of gene coexpression occurred in two metabolic pathways involved in lycopene and flavonoid biosynthesis. Independent experimental verification of the findings for six selected genes was done using quantitative real-time polymerase chain reaction. Our findings suggest that differential coexpression may assist in the investigation of key regulatory steps in metabolic pathways. The approaches and results reported here will be useful to prioritize candidate genes for further functional genomics studies of tomato metabolism.

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KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data

Cited by 67 publications

References 31 publications

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

Multiomics in Grape Berry Skin Revealed Specific Induction of the Stilbene Synthetic Pathway by Ultraviolet-C Irradiation

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

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