ArticleBioinformation2013
Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.
Article in Bioinformation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Transcriptional regulation modulates nitrate uptake and utilization ofFrontiers in plant science · 2026Article
- Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought.Frontiers in plant science · 2023Article
- Transcriptome and association mapping revealed functional genes respond to drought stress inFrontiers in plant science · 2022Article
- Photosynthetic Carbon Fixation and Sucrose Metabolism Supplemented by Weighted Gene Co-expression Network Analysis in Response to Water Stress in Rice With Overlapping Growth Stages.Frontiers in plant science · 2022Article
- Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle.Frontiers in genetics · 2021Article
- Comparative Transcriptome Analysis of DifferentInternational journal of molecular sciences · 2020Article
- Identification of Gene Modules and Hub Genes Involved in Mastitis Development Using a Systems Biology Approach.Frontiers in genetics · 2020Article
- A Protein-Linger Strategy Keeps the Plant On-Hold After Rehydration of Drought-StressedFrontiers in plant science · 2019Article
- Smoking and drinking influence the advancing of ischemic stroke disease by targeting PTGS2 and TNFAIP3.Experimental and therapeutic medicine · 2018Article
- Two-dimensional analysis provides molecular insight into flower scent of Lilium 'Siberia'.Scientific reports · 2018Article
- Multifunctional RNA Binding Protein OsTudor-SN in Storage Protein mRNA Transport and Localization.Plant physiology · 2017Article
- Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought ineLife · 2017Article
- Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.Rice (New York, N.Y.) · 2016Article
- Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.BMC bioinformatics · 2016Article
- Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice.Frontiers in plant science · 2015Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.
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