Table 3.

List of developmental stage-specific biological processes over-represented (FDR < 0.05) for up-regulated DEGs in TM-1 (TM-1 vs. im mutant)

Developmental stage	GO annotation	Functional categories	FDR
13 DPA	GO:0010200	Response to chitin	6.8E-08
	GO:0050832	Defense response to fungus	3.9E-02
16 DPA	GO:0009086	Methionine biosynthetic process	8.0E-06
	GO:0030244	Cellulose biosynthetic process	9.9E-04
	GO:0009834	Secondary cell wall biogenesis	3.2E-03
	GO:0010417	Glucuronoxylan biosynthetic process	4.1E-03
	GO:0006529	Asparagine biosynthetic process	4.1E-03
	GO:0010248	Establishment or maintenance of transmembrane electrochemical gradient	5.4E-03
	GO:0010951	Negative regulation of endopeptidase activity	5.4E-03
	GO:0015992	Proton transport	1.4E-02
	GO:0043617	Cellular response to sucrose starvation	2.0E-02
	GO:0007047	Cellular cell wall organization	2.4E-02
	GO:0019305	dTDP-rhamnose biosynthetic process	3.2E-02
19 DPA	GO:0005985	Sucrose metabolic process	2.8E-04
	GO:0010417	Glucuronoxylan biosynthetic process	9.3E-03
	GO:0009834	Secondary cell wall biogenesis	2.5E-02
	GO:0009877	Nodulation	3.5E-02
	GO:0052386	Cell wall thickening	3.7E-02
22 DPA	NA	NA	NA
25 DPA	GO:0010200	Response to chitin	5.2E-28
	GO:0050832	Defense response to fungus	2.4E-04
	GO:0006351	Transcription, DNA-dependent	2.5E-03
	GO:0009725	Response to hormone stimulus	5.2E-03
	GO:0045087	Innate immune response	4.1E-02
	GO:0009409	Response to cold	4.3E-02

NA, no result.

FDR, false discovery rate.