TABLE 1

Functional enrichment analyses of GO terms and PFAM domains of significant differentially expressed genes between treatments along the time series of Rhodonia placenta growing on unmodified radiata pine and three different levels of modification with furfuryl alcohol

Treatment comparisonaNo. of DE genesGO term(s) and/or PFAM domain(s)Frequency (no. of genes/total no. [%])Adjusted P valueDescriptionbCommentc
DOWN WPG4–UP unmodified38No enrichment
UP WPG4–DOWN unmodified32GO:00082708/562 (1.42)4.699815e−03MFZinc ion binding
GO:00164918/736 (1.09)3.389974e−02MFOxidoreductase activity
PF00107.214/76 (5.26)1.536767e−02Zinc-binding dehydrogenase
UP WPG24–DOWN unmodified228GO:001649140/736 (5.43)9.508001e−13MFOxidoreductase activity
GO:005511446/1,163 (3.96)5.487584e−10BPOxidation-reduction process
PF00107.2112/76 (15.79)4.007640e−07Zinc-binding dehydrogenase
PF13602.17/30 (23.33)1.059814e−04Zinc-binding dehydrogenase
PF00106.2013/198 (6.57)3.016412e−03Short-chain dehydrogenase
PF08659.511/142 (7.75)3.531839e−03KR domain
PF13561.19/105 (8.57)1.170520e−02Zinc-binding dehydrogenase
DOWN WPG24–UP unmodified241No enrichment
UP WPG37–DOWN unmodified907GO:001649188/736 (11.96)6.355618e−19MFOxidoreductase activity
GO:0055114108/1,163 (9.29)2.403803e−15BPOxidation-reduction process
GO:001670538/326 (11.66)1.483503e−06MFOxidoreductase activity
GO:005508546/490 (9.39)2.946082e−05BPTransmembrane transport
GO:000550638/367 (10.35)3.882514e−05MFIron ion binding
GO:002003740/419 (9.55)1.559430e−04MFHeme binding
GO:000815249/664 (7.38)1.270725e−02BPMetabolic process
GO:001018110/54 (18.52)3.305432e−02MFFMN binding
PF08659.527/142 (19.01)7.135697e−08KR domain
PF00106.2030/198 (15.15)2.054525e−06Short-chain dehydrogenase
PF00107.2117/76 (22.37)1.773561e−05Zinc-binding dehydrogenase
PF07690.1129/222 (13.06)1.097127e−04Major facilitator family
PF00067.1735/309 (11.33)2.032395e−04Cytochrome P450
PF13417.19/24 (37.50)3.098329e−04Glutathione S-transferase
PF13561.118/105 (17.14)5.010722e−04Zinc-binding dehydrogenase
PF00724.158/24 (33.33)3.857038e−03NADH:flavin oxidoreductase
PF13602.18/30 (26.67)2.424490e−02Zinc-binding dehydrogenase
DOWN WPG37–UP unmodified1,125GO:000651118/86 (20.93)1.690517e−03BPUbiquitin-dependent protein catabolic process
GO:00058399/23 (39.13)2.523168e−03CCProteasome core complex
GO:00516039/23 (39.13)2.523168e−03BPProteolysis involved in cellular protein catabolic process
GO:00197736/10 (60.00)5.541878e−03CCProteasome core complex, alpha-subunit complex
GO:00041756/11 (54.55)1.158001e−02MFEndopeptidase activity
GO:00042989/28 (32.14)1.630679e−02MFThreonine-type endopeptidase activity
GO:00331785/8 (62.50)2.652523e−02CCProton-transporting two-sector ATPase complex, catalytic domain
PF10584.46/8 (75.00)1.571873e−03Proteasome A_N
PF00227.219/21 (42.86)2.650923e−03Proteasome
PF08477.816/68 (23.53)5.702283e−03Ras of complex, Roc domain of DAP-kinase
PF00009.2213/49 (26.53)9.992408e−03GTP-binding elongation factor family, EF-Tu/EF-1A subfamily
PF00025.1616/74 (21.62)1.783714e−02ADP-ribosylation factor
PF00071.1715/71 (21.13)4.220867e−02Ras subfamily
PF00928.165/8 (62.50)4.438262e−02Adaptor complexes medium subunit domain
PF01399.227/17 (41.18)4.515427e−02PCI domain
  • a Treatments are weight percent gain (WPG) of wood of 4, 24, and 37%. Unmodified indicates unmodified wood. UP, upregulated; DOWN, downregulated.

  • b Description indicates gene ontology variables. MF, molecular function; BP, biological process; CC, cellular component.

  • c FMN, flavin mononucleotide; DAP, death-associated protein.