Table IV. Assignment of transcripts whose abundance decreased 3-fold or more to functional categories using DAVID.
The 741 gene transcripts that declined in abundance 3-fold or more were characterized. Selected significantly enriched functional clusters are shown together with the term(s) most representative of each cluster. Only those term(s) showing a significant change (P ≤ 0.05) after correction for multiple testing by the Benjamini-Hochberg (BH) method are shown. Category, gene count, fold enrichment (FE), and BH values are for the term in the cluster indicated by the asterisk. For genes in each cluster, see Supplemental Table S12. %C is the percentage of transcripts in the term representative of the cluster that were affected by at least one of the treatments affecting tissue carbohydrate status.
| CES | Category | Term | FE | Gene Count | BH | %C |
|---|---|---|---|---|---|---|
| 21.95 | GOTERM_CC_FAT | Chloroplast | 1.9 | 248 | 9.9E-26 | 37 |
| 7.27 | GOTERM_BP_FAT | Protein folding*, chaperone | 3.5 | 30 | 3.5E-6 | 63 |
| 7.02 | GOTERM_CC_FAT | Ribosomal protein | 3.9 | 38 | 4.0E-10 | 71 |
| 6.83 | SP_PIR_KEYWORDS | Amino acid biosynthesis | 4.1 | 17a | 2.3E-3 | 53 |
| 5.56 | GOTERM_CC_FAT | Cell wall | 2.2 | 56 | 7.2E-7 | 57 |
| 4.99 | GOTERM_CC_FAT | Thylakoid | 2.4 | 50 | 1.8E-7 | 20 |
| 5.01 | SP_PIR_KEYWORDS | Nucleosome core*, histone core, DNA packaging | 11 | 14 | 9.7E-9 | 79 |
| 4.06 | GOTERM_BP_FAT | Starch biosynthetic process | 11 | 6 | 5.3E-3 | 33 |
| 3.62 | GOTERM_BP_FAT | Carbohydrate catabolic process, glycolysis* | 4.9 | 13 | 5E-4 | 46 |
| 3.25 | GOTERM_BP_FAT | Microtubule | 5.1 | 13 | 1.8E-4 | 31 |
| 2.83 | GOTERM_BP_FAT | Glucan catabolic process | 6.8 | 9 | 1.4E-3 | 44 |
| 2.46 | GOTERM_BP_FAT | Fatty acid metabolic process | 2.6 | 19 | 8.7E-3 | 53 |
| 2.43 | INTERPRO | Glycoside hydrolase*, subgroup, catalytic core | 3.5 | 17 | 9.0E-3 | 35 |
| 2.40 | GOTERM_MF_FAT | Transaminase activity | 5.0 | 9 | 4.8E-2 | 56 |
| 2.33 | SP_PIR_KEYWORDS | Chlorophyll biosynthesis | 8.2 | 6 | 2.2E-2 | 0 |
| 1.91 | GOTERM_MF_FAT | Flavoprotein*, FAD binding | 3.2 | 10 | 2.7E-2 | 40 |
| 1.87 | SP_PIR_KEYWORDS | Cell wall biogenesis/degradation | 2.3 | 17 | 2.6E-2 | 41 |
| 1.83 | GOTERM_CC_FAT | Mitochondrial matrix | 3.3 | 10 | 1.5E-2 | 80 |
| 1.80 | SP_PIR_KEYWORDS | Isomerase | 3.9 | 19 | 4.9E-5 | 19 |
| 1.78 | GOTERM_BP_FAT | DNA replication | 3.8 | 16 | 6.2E-4 | 81 |
Eleven genes identified by DAVID and a further six identified by MapMan were included.