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Table 2 Enriched GO terms and their average correlations (Pearson r) with Vvgai1 expression levels in the shoot, leaf and root transcriptome

From: RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines

Tissue Class Representative GO annotation GO ID Enrichment FDR (log10)b Ave r pval (log10)c Notable genesd
GO cluster term a
Shoot Negatively correlated 1 amino sugar catabolic process GO:0046348 3.4 5.77 MAPK3, MATE EFFLUX, ATCHITIV, ATCHIA
1 cell wall macromolecule catabolic process GO:0016998 3.66 5.65
1 hormone catabolic process GO:0042447 3.01 3.41
2 cellular process GO:0009987 4.22 4.58  
3 response to red light GO:0010114 3.6 5.47 PR4, YSL3, GA2ox1, PRR7, BES1, LAC1, GRF5, DWARF4, TEMPRANILLO 2
3 response to chemical GO:0042221 3.05 4.63
3 response to abiotic stimulus GO:0009628 4.46 4.58
4 developmental process GO:0032502 3.7 4.85  
7 floral meristem determinacy GO:0010582 3.01 5.64 SPLs, VvSVP, ACO4, CKX, CKX5, PRX66
7 anatomical structure development GO:0048856 3.49 5.11
Leaf Positively correlated 1 phenylpropanoid metabolic process GO:0009698 12.48 19.72 FLS1, ATCHS, 2-ODD, UGT86A2
1 aromatic compound biosynthetic process GO:0019438 3.8 12.46
10 oxidation-reduction process GO:0055114 6.01 15.09 CCD1, MES10,CAT2
10 secondary metabolic process GO:0019748 6.07 13.8
Negatively correlated 1 DNA replication initiation GO:0006270 4.7 4.05 CDC45, MCM2, GRFs, MYB59, NAC71, WRKY 57
1 polysaccharide metabolic process GO:0005976 2.86 9.22
10 lipid metabolic process GO:0006629 2.74 9.77  
7 regionalization GO:0003002 4.68 10.59 SHR, YABBY1, AS1, CIB4, DWARF4
7 shoot system morphogenesis GO:0010016 3.19 9.57
7 pattern specification process GO:0007389 5.49 9.56
8 chromatin organization GO:0006325 2.63 4.81 CDC45, MCM2
Root Positively correlated 1 toxin catabolic process GO:0009407 3.52 6.66 SCR 21, VvDELLA1, VvDELLA2, PIF1, KNAT3, ARF16, ARF11, VvTFL1
1 phenylpropanoid metabolic process GO:0009698 12.48 5.07
  cellular biosynthetic process GO:0044249 3.8 4.84
1 hydrogen peroxide catabolic process GO:0042744 4.42 4.38
3 ethylene-activated signaling pathway GO:0009873 3.96 6.9 KO1, GA3ox, GA20ox1, GASA6, LRR family, UMAMIT42
3 response to chemical GO:0042221 19.33 4.93
3 response to stress GO:0006950 23.53 4.74
3 response to abiotic stimulus GO:0009628 4.01 4.36
7 coenzyme A metabolic process GO:0015936 4.34 6.83 PIF1, VvTFL1, C
4, MAP65–6, TUB8, SHR,CYP722A1, FLA4, MFS family,
7 cell recognition GO:0008037 3.31 5.15
7 indole-containing compound metabolic process GO:0042430 3.07 4.69
7 organic acid metabolic process GO:0006082 10.66 4.44
Negatively correlated 1 gene expression GO:0010467 3.37 4.88 CHS, LACASSE, 2-ODD, AP2/ERF, WRKY
1 cellular macromolecule biosynthetic process GO:0034645 4.29 4.78
1 cellular biosynthetic process GO:0044249 3.33 4.64
3 gibberellic acid mediated signaling pathway GO:0009740 6.55 8.79 PIN3, EIN3, ARR5, ARR9, OMR1, ACS1
3 ethylene-activated signaling pathway GO:0009873 3.55 6.72
3 response to red light GO:0010114 5.24 6.31
3 response to chemical GO:0042221 4.07 5.18
3 response to abiotic stimulus GO:0009628 9.32 4.83
7 anatomical structure development GO:0048856 4.39 4.46  
4 developmental process GO:0032502 3.96 4.4  
5 localization GO:0051179 4.49 3.87  
6 metabolic process GO:0008152 9.78 4.19  
9 response to stimulus GO:0050896 6.39 4.61  
  1. aGO cluster term: 1:Aromatic compound catabolism; 2:Cellular process; 3:Detoxification of nitrogen compound; 4;Developmental process; 5:Localization; 6:Metabolism; 7:Pattern specification process; 8:Protein polymerization; 9:Response to stimulus; and 10:Secondary metabolism
  2. bEnrichment pval (log10 scale) as determined by PlantMet GenMap
  3. cAverage expression correlation (Pearson’s r pval (log10 scale)) of the member genes with the expression level of Vvgail in the enriched GO term
  4. dWhile these genes were listed under a specific GO cluster, many of them were present in other clusters as well