Table 2.

List of selected GO terms, their IDs, log₂FCs (6 h 22°C versus 3 h 22°C + 3 h 37°C), P-values, the number of detected genes within the GO-term, and the number of DEGs (upregulated and downregulated) within the term

GO ID	GO term	log2FC	P-value	Genes	DEG	DEG
					up	down
Molecular function
GO:0043621	Functions in protein self-association	4.09	1.4E−07	126	47	5
GO:0051879	Functions in Hsp90 protein binding	3.38	9.8E−08	21	12	0
GO:0051082	Has unfolded protein binding	2.20	5.7E−07	225	102	1
GO:0009916	Has alternative oxidase activity	1.44	7.1E−07	8	4	0
GO:0004765	Has shikimate kinase activity	1.06	0.0006	3	2	0
GO:0030628	Has pre-mRNA 3′-splice site binding	1.06	2.2E−05	20	7	0
GO:0000064	Has l-ornithine transmembrane transporter activity	−1.07	8.3E−05	5	0	2
GO:0005476	Has carnitine:acyl carnitine antiporter activity	−1.08	9.4E−05	3	0	2
GO:0008792	Has arginine decarboxylase activity	−1.35	9.2E−06	4	0	3
GO:0005244	Has voltage-gated ion channel activity	−1.46	0.0029	3	0	2
GO:0038198	Has auxin receptor activity	−2.01	0.0005	2	0	2
Cellular component
GO:0089701	Located in U2AF	1.29	1.4E−05	18	7	0
Biological process
GO:0009061	Involved in anaerobic respiration	9.36	2.6E−05	2	2	0
GO:0061077	Involved in chaperone-mediated protein folding	3.27	8.4E−07	33	11	2
GO:0010187	Involved in negative regulation of seed germination	2.73	5.1E−06	28	11	1
GO:0006457	Involved in protein folding	2.26	5.4E−07	202	97	1
GO:0048026	Involved in positive regulation of mRNA splicing, via spliceosome	1.80	1.0E−06	11	2	0
GO:0009852	Involved in auxin catabolic process	1.72	4.6E−05	2	1	0
GO:0000302	Involved in response to ROS	1.68	6.5E−08	76	46	0
GO:0034605	Involved in cellular response to heat	1.65	1.7E−06	47	20	0
GO:0009408	Involved in response to heat	1.29	6.6E−08	266	116	10
GO:0010600	Involved in regulation of auxin biosynthetic process	1.17	0.0032	4	3	0
GO:0010508	Involved in positive regulation of autophagy	1.11	7.8E−06	14	3	0
GO:0043618	Involved in regulation of transcription from RNA polymerase II promoter in response to stress	1.06	1.3E−05	22	9	0
GO:0033388	Involved in putrescine biosynthetic process from arginine	−1.33	9.6E−06	6	0	3
GO:0071456	Involved in cellular response to hypoxia	0.743	7.12E−07	211	67	11
GO:0009446	Involved in putrescine biosynthetic process	−1.33	9.6E−06	6	0	3
GO:0006527	Involved in arginine catabolic process	−1.33	9.8E−06	7	0	3

A selection of GO terms grouped by sub-ontologies (molecular function, cellular component, and biological process) that show a strong log₂FC between pollen tubes grown for 6 h at 22°C and tubes grown for 3 h at 22°C followed by 3 h at 37°C. GO terms were quantified summing RPKM values of all detected genes within one GO term (number of genes is given) for the respective condition (6 h 22°C or 3 h 22°C + 3 h 37°C) and log₂FC of the summed RPKMs was calculated. P-values were calculated using Student’s t test on summed RPKM values of the two conditions. Number of DEGs (log₂FC > |1|, FDR < 0.005 according to DE analysis with EdgeR, Supplemental Datasets S12–S15) within the GO term are given.