Gene Expression Profiling Using DNA Microarrays

Maruyama, Kyonoshin; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

doi:10.1007/978-1-62703-580-4_20

Cited by 9 publications

(9 citation statements)

References 14 publications

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“…Raw data were analyzed using GeneSpring GX software, version 12.0 (Agilent Technologies). Expression log ratios and the Benjamini and Hochberg FDR P values were calculated using GeneSpring GX (Maruyama et al, 2014). The microarray design and data were deposited at MIAMExpress (accession nos.…”

Section: Microarray Analysismentioning

confidence: 99%

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

et al. 2014

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Correlations between gene expression and metabolite/phytohormone levels under abiotic stress conditions have been reported for Arabidopsis (Arabidopsis thaliana). However, little is known about these correlations in rice (Oryza sativa 'Nipponbare'), despite its importance as a model monocot. We performed an integrated analysis to clarify the relationships among cold-and dehydrationresponsive metabolites, phytohormones, and gene transcription in rice. An integrated analysis of metabolites and gene expression indicated that several genes encoding enzymes involved in starch degradation, sucrose metabolism, and the glyoxylate cycle are upregulated in rice plants exposed to cold or dehydration and that these changes are correlated with the accumulation of glucose (Glc), fructose, and sucrose. In particular, high expression levels of genes encoding isocitrate lyase and malate synthase in the glyoxylate cycle correlate with increased Glc levels in rice, but not in Arabidopsis, under dehydration conditions, indicating that the regulation of the glyoxylate cycle may be involved in Glc accumulation under dehydration conditions in rice but not Arabidopsis. An integrated analysis of phytohormones and gene transcripts revealed an inverse relationship between abscisic acid (ABA) signaling and cytokinin (CK) signaling under cold and dehydration stresses; these stresses increase ABA signaling and decrease CK signaling. High levels of Oryza sativa 9-cis-epoxycarotenoid dioxygenase transcripts correlate with ABA accumulation, and low levels of Cytochrome P450 (CYP) 735A transcripts correlate with decreased levels of a CK precursor in rice. This reduced expression of CYP735As occurs in rice but not Arabidopsis. Therefore, transcriptional regulation of CYP735As might be involved in regulating CK levels under cold and dehydration conditions in rice but not Arabidopsis.Land plants must mount suitable responses to overcome the adverse effects of water stress caused by either drought or low-temperature conditions (Levitt, 1980). Among the external stresses, water stress is one of the most important limitations of crop productivity (Bartels and Sunkar, 2005). Discoveries of useful genes for molecular breeding using metabolomics and transcriptomics promise to facilitate the improvement of crop yields under water stress conditions. It is important to identify plant metabolites and transcripts that respond to water stress to determine the essential steps in molecular processes related to the effective adaptation of plants to stress conditions. Metabolomic and transcriptomic data have provided much information on the metabolite, phytohormone, and transcript networks that control plant growth and development. Studies using mass spectrometry (MS) -based metabolomic techniques have identified and characterized many stress-responsive metabolites

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Section: Microarray Analysismentioning

confidence: 99%

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

et al. 2014

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“…DNA microarray is one of the most popular technologies for gene expression profiling used in the past 15 years [ 28 , 42 , 46 , 50 , 68 ]. In this study we presented the development and the validation of the microarray CAZyChip dedicated to analyze the bacterial glycoside hydrolase expression.…”

Section: Discussionmentioning

confidence: 99%

“…DNA microarrays are widely used to profile gene expression and represent a relevant tool to study expression of key enzymes and monitor physiological changes of pure cultures or microbial communities [ 12 , 18 , 28 , 42 , 46 , 50 , 68 ]. This approach can also be useful to link microbial diversity to ecosystem processes and functions [ 22 , 29 , 67 ].…”

Section: Introductionmentioning

confidence: 99%

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems

et al. 2016

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BackgroundMicroorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans.ResultsThis DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota.ConclusionsThe CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2988-4) contains supplementary material, which is available to authorized users.

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“…In the past few decades, increasing evidence has confirmed that microarrays and bioinformatics analyses could be performed to evaluate potential biomarkers in multiple diseases at molecular levels . Gene expression profiling (GEP) is an effective way to identify important molecules and mechanistic pathways . GEP has been carried out to compare the differently expressed genes between ALT‐negative and ALK‐positive ALCL samples, improving the diagnosis and classification of ALCLs.…”

Section: Introductionmentioning

confidence: 99%

“…8,9 Gene expression profiling (GEP) is an effective way to identify important molecules and mechanistic pathways. 10 GEP has been carried out to compare the differently expressed genes between ALT-negative and ALK-positive ALCL samples, 11 improving the diagnosis and classification of ALCLs. Super-enhancers were found in multiple adult T-cell leukemia/lymphoma (ATLL) but no expression in normal mature T cells by GFP, implicating involvement of those genes in ATLL pathogenesis.…”

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confidence: 99%

T‐cell lymphomas associated gene expression signature: Bioinformatics analysis based on gene expression Omnibus

Zhou

et al. 2018

European J of Haematology

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Gene Expression Profiling Using DNA Microarrays

Cited by 9 publications

References 14 publications

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems

T‐cell lymphomas associated gene expression signature: Bioinformatics analysis based on gene expression Omnibus

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