Systems-Based Approach to the Analyses of Plant Functions: Conceptual Understanding, Implementation, and Analysis

Yadav, Brijesh Singh; Singh, Amit Kumar; Kushwaha, Sandeep

doi:10.1007/978-3-319-67156-7_2

Cited by 5 publications

(3 citation statements)

References 58 publications

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“…Analysis of metabolic pathways enrichment contributes to the systems-biology approach of understanding stress biology of plants [83]. Here, our KEGG pathway enrichment analysis revealed that the nitrogen metabolism pathway was the most significantly ( p < 0.01) enriched in the tolerant line YE8112 under drought stress conditions (Figure 5A).…”

Section: Discussionmentioning

confidence: 91%

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

Zenda

Liu

Wang

et al. 2019

IJMS

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To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R2 = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.

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Section: Discussionmentioning

confidence: 91%

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

Zenda

Liu

Wang

et al. 2019

IJMS

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“…The system-based molecular networks of accessible repurposed therapeutic options and their prospective targets give comprehensive information on the encoded proteins, genomic sequences and metabolites associated with stress progression ( Yadav et al, 2016 ). The information for the disease’s genomics, proteomics, and metabolomics investigations was gathered from the research publications or via genome-wide association sequencing (GWAS) and next-generation sequencing studies ( Yadav et al, 2017 ). In contrast to virtual screening, where target moieties are already known, systems biology possesses the ability to identify undiscovered target m in the pathogen’s genome and metabolome ( Yadav and Tripathi, 2018 ).…”

Section: Recent Systems Biology and Network-based Approaches For Drug...mentioning

confidence: 99%

System and network biology-based computational approaches for drug repositioning

Pandita

Parihar

Parihar³

et al. 2022

Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection

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“…The system-based molecular networks of the available repurposable drug candidates with their potential targets provide the complete information about the genes expressed, the encoded proteins and metabolites involved during progression of the stress (Yadav et al 2016 ). The data used for the genomics, proteomics and metabolomics analysis of the disease are either retrieved from the available literature or obtained from next generation sequencing (NGS) and genome-wide association sequencing (GWAS) analyses (Yadav et al 2017 ). Contrary to the virtual screening approach, in which targets are already known from the beginning, system biology has capability to predict unknown targets in the genome and metabolome of the pathogen (Yadav and Tripathi 2018 ).…”

Section: Systems Biology-based Approaches For Identification Of Targementioning

confidence: 99%

Molecular targets and system biology approaches for drug repurposing against SARS-CoV-2

2020

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Background COVID-19, a pandemic declared by WHO, has infected about 39.5 million and killed about 1.1 million people throughout the world. There is the urgent need of more studies to identify the novel drug targets and the drug candidates against it to handle the situation. Main body To virtually screen various drugs against SARS-CoV-2, the scientists need the detail information about the various drug targets identified till date. The present review provides the information about almost all the drug targets, including structural and non-structural proteins of virus as well as host cell surface receptors, that can be used for virtual screening of drugs. Moreover, this review also focuses on the different network analysis tools that have been used for the identification of new drug targets and candidate repurposable drugs against SARS-CoV-2. Conclusion This review provides important insights of various drug targets and the network analysis tools to young bioinformaticians and will help in creating pace to the drug repurposing strategy for COVID-19 disease.

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Systems-Based Approach to the Analyses of Plant Functions: Conceptual Understanding, Implementation, and Analysis

Cited by 5 publications

References 58 publications

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

System and network biology-based computational approaches for drug repositioning

Molecular targets and system biology approaches for drug repurposing against SARS-CoV-2

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