Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.)
Abstract
:1. Introduction
2. Methods
2.1. Prerequisites
2.2. Congruent Gene Correlations
2.3. Robustness of a Relation between Genes
2.4. The “Gene2Gene” Algorithm
- The genes of interest, say a set of “g” gene identifiers.
- The genotypes (or accessions) where the estimation will be performed, i.e., a set of “a” genotypes.
- A threshold for the FDR, “f”.
- A threshold for the minimum value of Pearson’s determination coefficient, “”.
- A threshold to eliminate putative regression outliers, “q”.
- The minimum number of genotypes where the gene relation must be found to be reported in the output, “x” ().
2.5. Constructing GFN: A Bottom-Up Approach
3. Results
3.1. Data Analyses
3.1.1. GFN for Three Biological Processes (BPs)
3.1.2. A Meta-Network
3.2. Finding Transcription Factors for Hub Genes
3.3. Sensitivity Analyses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
BP | Biological Process |
celcy | Cell cycle (BP) |
D | Domesticated accession (genotype) |
DAA | Days After Anthesis |
FDR | False Discovery Rate |
GCN | Gene Coexpression Network |
GFN | Gene Functional Network |
MN | Meta Network |
rep | Reproduction (BP) |
SEP | Standardized Expression Profile |
TF | Transcription Factor |
W | Wild accession (genotype) |
vir | Response to virus (BP) |
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BP | In | Out | % Out/In | Con. | ||
---|---|---|---|---|---|---|
celcy | 352 | 29 | 8 | 81 | 0.9859 | 0.00729 |
rep | 228 | 10 | 4 | 29 | 0.9934 | 0.00257 |
vir | 33 | 4 | 12 | 6 | 0.9936 | 0.00126 |
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Flores-Díaz, A.; Escoto-Sandoval, C.; Cervantes-Hernández, F.; Ordaz-Ortiz, J.J.; Hayano-Kanashiro, C.; Reyes-Valdés, H.; Garcés-Claver, A.; Ochoa-Alejo, N.; Martínez, O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.). Plants 2023, 12, 1148. https://doi.org/10.3390/plants12051148
Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.). Plants. 2023; 12(5):1148. https://doi.org/10.3390/plants12051148
Chicago/Turabian StyleFlores-Díaz, Alan, Christian Escoto-Sandoval, Felipe Cervantes-Hernández, José J. Ordaz-Ortiz, Corina Hayano-Kanashiro, Humberto Reyes-Valdés, Ana Garcés-Claver, Neftalí Ochoa-Alejo, and Octavio Martínez. 2023. "Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Capsicum annuum L.)" Plants 12, no. 5: 1148. https://doi.org/10.3390/plants12051148