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. 2015 Jan 22;66(5):1511–1526. doi: 10.1093/jxb/eru516

Table 1.

DAVID functional analysis: Functional annotation chart (FACH) of AVG genes up- and down-regulated (fold change >2) recognized in DAVID database Functional category, terms and genes with accession number, percentage of gene included, P value, fold enrichment, and statistical significance (Bonferroni, Benjamini, and FDR).

AVG
GO Category Up-regulated
(162 recognised)		 % P value Fold enrichment Statistical significance
GOTERM_CC_FAT GO:0005576 extracellular region:
(X55193) 9612 protein
(Z15141) chitinase
(X55693) glycine-rich protein
(X79337) ribonuclease		 2.47 0.04 3.87 0.48, 0.48, 26.08
SP_PIR_KEYWORDS Nucleus:
(U22441) LeRAD51
(L28715) Ran protein/TC4 protein
(AJ011914) THY5 protein
(AF154003) pirin		 3.09 0.05 3.09 0.98, 0.98,44.21
GO Category Down-regulated
(160 recognised)		 % P value Fold enrichment (FE) Statistical significance
GOTERM_BP_FAT GO:0019748~secondary metabolic process:
(AF263101) 4-diphosphocytidyl-2-C- methyl-d-erythritol kinase
(X55195) chalcone synthase
(X55194) chalcone synthase
(X86452) lycopene beta-cyclase
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(EF581828) zeaxanthin epoxidase		 7.5 0.00 7.58 0.00, 0.00, 0.00
SP_PIR_KEYWORDS transit peptide:
(Z11999) 33kDa precursor protein of oxygen-evolving complex
(AF263101) 4-diphosphocytidyl-2-C- methyl-d-erythritol kinase
(M17558) chlorophyll a/b-binding protein precursor
(U66300) heat shock protein
(U50152) leucine aminopeptidase
(X86452) lycopene beta-cyclase
(Z21792) phospho-2-dehydro-3-deoxyheptonate aldolase
(X63007) photosystem II 23kDa protein
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(AF347664) translation initiation factor IF1 (EF581828) zeaxanthin epoxidase		 12. 0.00 3.55 0.00, 0.00, 0.02
GOTERM_BP_FAT GO:0006720~isoprenoid metabolic process; GO:0006721~terpenoid metabolic process; GO:0016114~terpenoid biosynthetic process;
GO:0008299~isoprenoid biosynthetic process:
(AF263101) 4-diphosphocytidyl-2-C-methyl-d- erythritol kinase
(X86452) lycopene beta-cyclase
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(EF581828) zeaxanthin epoxidase		 5.66 0.0001 8.12 0.02, 0.01, 0.14
UP_SEQ_FEATURE transit peptide:Chloroplast
(Z11999) 33kDa precursor protein of oxygen-evolving complex
(M17558) chlorophyll a/b-binding protein precursor
(U66300) heat shock protein
(U50152) leucine aminopeptidase
(X86452) lycopene beta-cyclase
(Z21792) phospho-2-dehydro-3-deoxyheptonate aldolase
(X63007) photosystem II 23kDa protein
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(AF347664) translation initiation factor IF1 (EF581828) zeaxanthin epoxidase		 10.38 0.0003 3.27 0.03, 0.03, 0.34
GOTERM_BP_FAT GO:0008610~lipid biosynthetic process
(AF263101) 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase
(U09026) lipoxygenase
(X86452) lycopene beta-cyclase
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(EF581828) zeaxanthin epoxidase		 6.60 0.0006 5.10 0.07, 0.02, 0.66
GOTERM_BP_FAT GO:0016109~tetraterpenoid biosynthetic process; GO:0016117 ~carotenoid biosynthetic process; GO:0016108~tetraterpenoid metabolic process; GO:0016116~carotenoid metabolic process carotenoid biosynthesis:
(X86452) lycopene beta-cyclase
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase		 3.77 0.01 7.58 0.62, 0.22, 8.72
GOTERM_BP_FAT GO:0042440~pigment metabolic process GO:0046148~pigment biosynthetic process
(X86452) lycopene beta-cyclase
(S36691) phytoene desaturase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase		 3.77 0.01 6.32 0.84, 0.31, 15.72
SP_PIR_KEYWORDS Isoprene biosynthesis
(AF263101) 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase		 2.83 0.03 9.56 0.93, 0.59, 26.46
SP_PIR_KEYWORDS Phosphoprotein
(X59146) 1-aminocyclopropane-1-carboxylate synthase
(AY269087) GAI-like protein
(M60166) H+-ATPase RG Solanum lycopersicum
(M17558) chlorophyll a/b-binding protein precursor
(X71900) histidine decarboxylase
(AY368907) molecular chaperone Hsp90-2		 5.66 0.03 3.02 0.95, 0.52, 28.77
SP_PIR_KEYWORDS Transferase
(AF263101) 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase
(X55195) chalcone synthase
(X55194) chalcone synthase
(Z21792) phospho-2-dehydro-3-deoxyheptonate aldolase
(EF534738) phytoene synthase
(BT012712) phytoene synthetase
(AJ006414) spermidine synthase		 6.60 0.05 2.39 0.99, 0.59, 40.62