Table 1.

Overrepresentation of protein groups in downregulated and upregulated proteins

GO typea	Group	Enrichment factorb	p‐Valuec
Downregulated (1015)d
MF	Phosphorelay Response Regulator Activity (GO:0000156)	5.91	3.61E−03
BP	Chlorophyll Biosynthetic Process (GO:0015995)	4.54	5.11E−05
CC	Photosystem I (GO:0009522)	4.04	1.00E−02
BP	Starch Biosynthetic Process (GO:0019252)	4.04	3.83E−02
CC	Stromule (GO:0010319)	3.73	4.18E−02
CC	Chloroplast Thylakoid Membrane (GO:0009535)	2.72	3.81E−15
BP	Photosynthesis (GO:0015979)	2.58	2.11E−05
BP	Response to Cytokinin (GO:0009735)	2.54	2.35E−05
CC	Chloroplast Stroma (GO:0009570)	2.33	3.22E−22
CC	Chloroplast Membrane (GO:0031969)	2.11	1.18E−02
Downregulated at G (241)
BP	Starch Biosynthetic Process (GO:0019252	10.01	9.61E−03
BP	Chlorophyll Biosynthetic Process (GO:0015995)	7.48	1.76E−02
Downregulated at LG (60)
BP	Photosystem II Assembly (GO:0010207)	37.49	5.18E−03
CC	Photosystem II Oxygen Evolving Complex (GO:0009654)	28.12	4.22E−03
BP	Photosynthesis, Light Harvesting (GO:0009765)	22.50	3.79E−02
Upregulated (2556)
BP	Defense Response to Other Organism (GO:0098542)	1.41	3.89E−02
BP	Cellular Catabolic Process (GO:0044248)	1.36	1.39E−02
CC	Cell Wall (GO:0005618)	1.35	2.04E−02
CC	Extracellular Region (GO:0005576)	1.35	2.73E−05
CC	Vacuole (GO:0005773)	1.32	1.35E−03
CC	Plasma Membrane (GO:0005886)	1.23	2.42E−04
CC	Endomembrane System (GO:0012505)	1.22	6.82E−03
BP	Defense Response to Other Organism (GO:0098542)	1.41	3.89E−02
BP	Cellular Catabolic Process (GO:0044248)	1.36	1.39E−02
CC	Cell Wall (GO:0005618)	1.35	2.04E−02
CC	Extracellular Region (GO:0005576)	1.35	2.73E−05

^aGO types: Cell Compartment (CC), Biological Process (BP), and Molecular Function (MF).

^bAs calculated by the Perseus software platform. Enrichment factor = [(Intersection size)·(Total size)]/[(Selection size)·(Category size)].

^cProteins that passed the ANOVA significance test (p < 0.05).

^dNumbers in brackets indicate the number of proteins in the analyzed group.