Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Collection and Pre-Processing
2.2. Screening and Identification of Differentially Expressed Genes
2.3. Weighted Gene Co-Expression Network Analysis
2.4. Identification of Hub Genes
2.5. GO and Pathway Functional Enrichment Analyses
2.6. Cis-Acting Element Analysis
2.7. Identification of Transcription Factor Families
2.8. Protein–Protein Interaction (PPI) Networks
2.9. Validation Analysis
3. Results
3.1. Pre-Processing and Identification of the Drought-Responsive Core DEGs
3.2. Co-Expression Analysis and Module Identification under Drought Stress
3.3. Identification of Hub Genes and Enrichment Analysis
3.4. Identification of Transcription Factors
3.5. Cis-Acting Elements Analysis and Motif Identification
3.6. Protein–Protein Interactions and Selection of Key Genes
3.7. Leave-One-Out Cross-Validation of Hub Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accession | Type | Platform | Control | Treatment | Tissue | Released |
---|---|---|---|---|---|---|
E-GEOD-40627 | Response to drought | GPL13674, Affymetrix | 3 | 3 | Leaf | 10 November 2012 |
E-GEOD-65553 | Response to drought | GPL13674, Affymetrix | 9 | 9 | Root | 2 July 2015 |
E-GEOD-29663 | Response to drought | GPL13674, Affymetrix | 3 | 3 | Leaf | 2 April 2012 |
Total samples | 30 |
Module Name | Number of Genes |
---|---|
Blue | 441 |
Brown | 258 |
Green | 128 |
Red | 99 |
Turquois | 911 |
Yellow | 220 |
Black | 68 |
Pink | 36 |
Motif Name | Motif Logo | E-Value | Width | Best Match in JASPAR and PLACE | Significant GO Terms Identified by GOMO |
---|---|---|---|---|---|
Motif 1 | 8.0 × 10−100 | 41 | MA1403.1 (BBR/BBC) | MF: transcription factor activity CC: nucleus CC: plasma membrane BP: regulation of transcription, DNA-dependent BP: protein amino acid phosphorylation | |
Motif 2 | 1.1 × 10−44 | 20 | MA1268.1 (Dof) | MF: transcription factor activity CC: nucleus MF: protein serine/threonine kinase activity BP: protein amino acid phosphorylation BP: regulation of transcription, DNA-dependent | |
Motif 3 | 9.6 × 10−27 | 15 | MA1268.1 (Dof) | MF: transcription factor activity BP: regulation of transcription CC: plasma membrane CC: nucleus BP: response to water deprivation | |
Motif 4 | 1.6 × 10−17 | 15 | MA1890.1 (C2H2) | CC: chloroplast MF: transcription factor activity BP: photosynthetic electron transport in photosystem I | |
Motif 5 | 1.7 × 10−5 | 15 | MA1403.1 (BBR/BBC) | MF: transcription factor activity CC: nucleus CC: plasma membrane BP: regulation of transcription, DNA-dependent MF: protein binding | |
Motif 6 | 1.4 × 10−10 | 21 | MA1281.1 (Dof) | MF: transcription factor activity CC: plasma membrane CC: nucleus BP: regulation of transcription BP: response to water deprivation | |
Motif 7 | 5.3 × 10−5 | 41 | MA0386.1 (Fox) | MF: transcription factor activity CC: endomembrane system BP: regulation of transcription, DNA-dependent BP: oligopeptide transport MF: protein heterodimerization activity | |
Motif 8 | 9.1 × 10−1 | 29 | MA1354.1 (MYB-related) | CC: chloroplast | |
Motif 9 | 1.9 × 10−3 | 27 | MA1892.1 (C2H2) | CC: chloroplast MF: transcription factor activity CC: nucleus BP: DNA replication initiation BP: developmental growth | |
Motif 10 | 1.1 × 10−4 | 21 | MA1723.1 (C2H2) | MF: transcription factor activity CC: nucleus BP: regulation of transcription, DNA-dependent CC: plasma membrane MF: protein binding | |
Motif 11 | 2.1 × 10−4 | 21 | MA1766.1 (MYB) |
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Shahriari, A.G.; Soltani, Z.; Tahmasebi, A.; Poczai, P. Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.). Genes 2022, 13, 1732. https://doi.org/10.3390/genes13101732
Shahriari AG, Soltani Z, Tahmasebi A, Poczai P. Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.). Genes. 2022; 13(10):1732. https://doi.org/10.3390/genes13101732
Chicago/Turabian StyleShahriari, Amir Ghaffar, Zahra Soltani, Aminallah Tahmasebi, and Péter Poczai. 2022. "Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.)" Genes 13, no. 10: 1732. https://doi.org/10.3390/genes13101732