Table 6.
The annotation of the hub genes with ≥7 co-expressed genes identified by WGCNA.
| Node | Num | P-value | Fold change | Gene annotation | GO term |
|---|---|---|---|---|---|
| LOC_Osm1g00580 | 63 | 5.80E-03 | 6.14 | ATP synthase F0 subunit 1 | ATP biosynthetic process |
| LOC_Osm1g00110 | 54 | 4.40E-03 | 10.73 | Cytochrome c oxidase subunit 3 | Respiratory electron transport chain |
| LOC_Osm1g00120 | 52 | 7.90E-03 | 9.79 | Hypothetical protein | ATP synthesis coupled proton transport |
| LOC_Os09g08910 | 48 | 3.42E-03 | 4.63 | ATP synthase subunit alpha | Response to stress |
| LOC_Os09g00999 | 46 | 2.76E-03 | 4.62 | Putative uncharacterized protein P0459B01.16 | Unannotated |
| LOC_Os04g16722 | 32 | 2.17E-03 | 4.85 | Uncharacterized protein ycf68 | Unannotated |
| LOC_Osm1g00370 | 13 | 2.48E-03 | 6.77 | ATP synthase F0 subunit 6 | ATP synthesis coupled proton transport |
| LOC_Osm1g00440 | 12 | 1.80E-03 | 6.37 | Ribosomal protein L2 | Translation |
| LOC_Os12g34108 | 9 | 8.80E-02 | 1.39 | ATP synthase protein 9 | Transporter activity |
| LOC_Osm1g00230 | 9 | 8.73E-03 | 7.19 | NADH dehydrogenase subunit 7 | Oxidation-reduction process |
| LOC_Os02g24614 | 8 | 1.48E-02 | 3.53 | DNA-directed RNA polymerase subunit beta | Transferase activity |
| LOC_Os12g33956 | 8 | 1.28E-02 | 3.19 | Maturase | Transferase activity |
| LOC_Os12g34094 | 8 | 8.04E-03 | 4.66 | NADH-ubiquinone oxidoreductase chain 4 | Generation of precursor metabolites and energy |
| LOC_Os06g16380 | 7 | 7.97E-03 | 8.51 | Expressed protein | Unannotated |
| LOC_Os12g34014 | 7 | 7.52E-03 | 10.62 | NADH-ubiquinone oxidoreductase chain 6 | Generation of precursor metabolites and energy |
| LOC_Osm1g00320 | 7 | 2.60E-02 | 5.29 | NADH dehydrogenase subunit 4 | Oxidation-reduction process |
| LOC_Osm1g00390 | 7 | 2.74E-02 | 10.18 | Ribosomal protein S13 | Translation |
| LOC_Osm1g00490 | 7 | 1.04E-02 | 3.03 | Maturase-related protein | mRNA processing |
The boldface in the “Node” column highlighted the genes located on the mitochondria genome. Num, is the number of co-expressed genes with the node gene in the first column; P-value, is the significance of the paired t-test of the gene expression between 37 pairs of deep roots and shallow roots in the same variety; Fold change, the average fold changes of the 37 pairs of gene expressions between the deep roots and shallow roots from the same variety. The boldface in the “GO Term” column highlighted the genes related to energy metabolism, and the italic highlighted the genes related to transcription and translation.