TABLE 3.
GO term enrichment analysis (by BP) of up- and downregulated genes identified by comparative RNA-seq analysis in X. dendrorhous strains
| GO ID | BP | Annotated | Significant | Expected | Rank in Classic Fisher | P (classic) | P (weight01) | |
| RNA-seq analysis of strain CBS.FLAG.SRE1N compared with the WT CBS 6938 (DEGs: 1,421 genes. UP: 622, DW: 799) | ||||||||
| UP | ||||||||
| 1 | GO:0006696 | Ergosterol biosynthetic process | 14 | 9 | 1.43 | 3 | 1.3E-06 | 1.3E-06 |
| DW | ||||||||
| 1 | GO:0055114 | Oxidation-reduction process | 409 | 91 | 44.58 | 1 | 6.8E-13 | 4.9E-13 |
| 2 | GO:0055085 | Transmembrane transport | 349 | 64 | 38.04 | 3 | 7.6E-06 | 8.1E-08 |
| 3 | GO:0015074 | DNA integration | 52 | 18 | 5.67 | 2 | 4.0E-06 | 4.0E-06 |
| RNA-seq analysis of strain CBS.cyp61− compared with the WT CBS 6938 (DEGs: 661 genes. UP: 337, DW: 324) | ||||||||
| UP | ||||||||
| 1 | GO:0006696 | Ergosterol biosynthetic process | 14 | 8 | 0.83 | 4 | 3.0E-07 | 3.0E-07 |
| 2 | GO:0006334 | Nucleosome assembly | 11 | 5 | 0.66 | 33 | 2.5E-04 | 2.5E-04 |
| 3 | GO:0007018 | Microtubule-based movement | 17 | 6 | 1.01 | 34 | 2.9E-04 | 2.9E-04 |
| 4 | GO:0055114 | Oxidation-reduction process | 409 | 41 | 24.36 | 36 | 3.8E-04 | 7.4E-04 |
| DW | ||||||||
| 1 | GO:0015074 | DNA integration | 52 | 15 | 2.08 | 1 | 6.0E-10 | 6.0E-10 |
| 2 | GO:0055114 | Oxidation-reduction process | 409 | 32 | 16.32 | 3 | 9.2E-05 | 2.0E-04 |
| RNA-seq analysis of strain CBS.cyp61−.sre1− compared with strain CBS.cyp61− (DEGs: 469 genes. UP: 230, DW: 239) | ||||||||
| UP | ||||||||
| 1 | GO:0055114 | Oxidation-reduction process | 409 | 31 | 11.21 | 1 | 3.8E-08 | 4.1E-08 |
| 2 | GO:0055085 | Transmembrane transport | 349 | 22 | 9.56 | 2 | 1.2E-04 | 2.2E-06 |
| DW | ||||||||
| 1 | GO:0006696 | Ergosterol biosynthetic process | 14 | 8 | 0.57 | 5 | 1.5E-08 | 1.5E-08 |
| 2 | GO:0007018 | Microtubule-based movement | 17 | 6 | 0.69 | 20 | 3.5E-05 | 3.5E-05 |
| 3 | GO:0055114 | Oxidation-reduction process | 409 | 31 | 16.69 | 26 | 3.4E-04 | 1.8E-04 |
| 4 | GO:0008610 | Lipid biosynthetic process | 92 | 18 | 3.75 | 4 | 1.5E-08 | 2.0E-04 |
| RNA-seq analysis of strain CBS.sre1− compared with the WT CBS 6938 (DEGs: 13 genes. UP: 3, DW: 10) | ||||||||
| DW | ||||||||
| 1 | GO:0006696 | Ergosterol biosynthetic process | 14 | 5 | 0.04 | 2 | 7.0E-11 | 7.0E-11 |
| 2 | GO:0008610 | Lipid biosynthetic process | 92 | 8 | 0.25 | 1 | 2.1E-12 | 1.0E-06 |
The enrichment analysis was performed with the topGO package. The table shows GO terms according to the “classic” and “weight01” algorithms and the “fisher” statistic; a P < 0.001 cut-off was used for the “weight01” algorithm. GO terms in the table were sorted by the P associated with the “weight01” algorithm. No significant results were found for the upregulated genes in strain CBS.sre1− compared with the WT CBS 6938. UP, upregulated genes; DW, downregulated genes.