Table 1. Significant over-representation of GO categories (BP and MF) among genes, which showed different transcription levels between all genes expressed on the microarray and the different experimental groups.
| Comparison | Category | Descriptiona | Foldb | Count (%)c | P-valued | Number of GO termsa |
|---|---|---|---|---|---|---|
| Backcross-moribund/backcross-healthy | BP | Generation of precursor metabolites and energy | 1.74 | 67 (10.2%) | 0.000 | 1 |
| BP | Translational elongation | 1.91 | 28 (4.2%) | 0.066 | 1 | |
| MF | Structural molecule activity | 1.49 | 65 (9.8%) | 0.022 | 1 | |
| MF | Hydrogen ion transporter activity | 1.86 | 28 (4.2%) | 0.047 | 1 | |
| Backcross-moribund/dwarf | BP | Generation of precursor metabolites and energy | 1.72 | 60 (10.1%) | 0.000 | 1 |
| BP | Translation | 1.84 | 70 (11.7%) | 0.022 | 2 | |
| MF | Structural molecule activity | 1.58 | 62 (10.4%) | 0.006 | 1 | |
| Backcross-moribund/normal | BP | Generation of precursor metabolites and energy | 1.78 | 63 (10.3%) | 0.000 | 1 |
| BP | Translational elongation | 2.07 | 28 (4.6%) | 0.010 | 1 | |
| MF | Cytoskeletal protein binding | 1.75 | 38 (6.2%) | 0.021 | 1 | |
| Backcross-healthy/dwarf | BP | Glycolysis | 21.08 | 6 (22.2%) | 0.001 | 1 |
| BP | Alcohol catabolic process | 15.17 | 6 (22.2%) | 0.009 | 1 | |
| BP | Carbohydrate catabolic process | 14.59 | 6 (22.2%) | 0.006 | 4 | |
| Backcross-healthy/normal | — | |||||
| Dwarf/normal | — | |||||
| All genes differentially expressed and backcross-moribund overexpressed genes | BP | Generation of precursor metabolites and energy | 2.09 | 62 (18.5%) | 0.00 | 1 |
| BP | Oxidation reduction | 1.76 | 50 (14.9%) | 0.00 | 1 | |
| BP | Electron transport chain | 2.12 | 30 (8.9%) | 0.00 | 1 | |
| BP | Phosphorylation | 1.82 | 29 (8.6%) | 0.05 | 1 | |
| MF | Catalytic activity | 1.24 | 148 (44%) | 0.00 | ||
| MF | Magnesium ion binding | 2.05 | 21 (6.3%) | 0.01 | ||
| MF | Ion transporter activity | 1.80 | 28 (8.2%) | 0.02 | 9 | |
| All genes differentially expressed and | BP | Translation | 1.41 | 69 (15.4%) | 0.001 | 1 |
| backcross-moribund underexpressed genes | BP | Gene expression | 1.29 | 136 (30.3%) | 0.000 | 1 |
| BP | Macromolecule metabolic process | 1.26 | 182 (40.4%) | 0.00 | 4 | |
| BP | RNA metabolic process | 1.45 | 48 (10.7%) | 0.033 | 2 | |
| MF | Structural constituent of ribosome | 1.48 | 8.9 (40%) | 0.029 | 1 | |
| MF | Nucleic acid binding | 1.32 | 86 (19.2%) | 0.016 | 2 | |
| All genes differentially expressed and | BP | Translation | 3.91 | 22 (48.9%) | 0.000 | 1 |
| essential genes differentially expressed | BP | Gene expression | 2.64 | 32 (71.1%) | 0.000 | 1 |
| BP | Macromolecule biosynthetic process | 2.08 | 30 (66.7%) | 0.002 | 6 | |
| BP | Protein metabolic process | 1.97 | 32 (71.9%) | 0.001 | 3 | |
| MF | Structural constituent of ribosome | 5.20 | 16 (35.6%) | 0.000 | 1 | |
| MF | Structural molecule activity | 3.25 | 16 (35.6%) | 0.002 | 1 |
Abbreviations: BP, biological process; GO, gene ontology; MF, molecular function.
Similar GO terms were grouped together as one category using the most inclusive GO term provided (for example, macromolecule metabolic process grouped within macromolecule biosynthetic process). Number of original GO terms in each category was written in number of GO terms column.
Fold enrichment values given by DAVID as compared to the background group (either genes expressed or all genes differentially expressed).
Number of unigenes in GO category and percentage of total.
Note that when more than one GO term were included in the same category, the P-value (Ease score (Bonferroni correction implemented by Huang et al., 2009)) was the mean P-values of all the GO terms.