Comparative Network Analysis of Redox-Responsive Gene Expression and Stress Signaling Pathways in Arabidopsis thaliana
Keywords:
Arabidopsis thaliana, Redox-responsive genes, Oxidative stress, Gene regulatory networks, Transcriptomic analysisAbstract
Leukemias Reactive oxygen species (ROS) play regulatory roles in plant development and adaptation to stress; however, the connections between the redox-responsive transcription processes and stress signaling networks are not fully understood. In this study, we suggest a bioinformatics tool based on comparative analysis of publicly available microarray data sets GSE80200 and GSE40574 from the NCBI Gene Expression Omnibus to explore these connections in the model plant A. thaliana. The flow includes expression preprocessing, differential expression analysis using limma, functional annotation, co-expression and protein association networks, hub-gene prioritization and Gene Ontology and KEGG enrichment. Comparisons of hydrogen peroxide and light resulted in 1,684, and 1,246 differentially expressed genes, respectively, and 2,118 were differentially expressed in the comparison of hydrogen peroxide with light in an illustrative simulation. All candidate regulators, except for ZAT12, showed coordinated hypothetical expression patterns, and the enriched processes highlighted were oxidative stress, glutathione metabolism, and MAPK signaling. These values are theoretical, not the results of evaluating datasets, and thus are not indicative of biological effects. The study adds a replicable analytical approach to measure shared and condition-specific redox responses. To test for robustness, cross-dataset concordance and sensitivity testing will be planned. Future implementation with the original expression measurements and independent functional validation is required to validate the molecular conclusions.
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