Table 1.

Gene ontology (GO) terms enriched amongst the jasmonic acid (JA)‐responsive genes in common dandelion (most specific GO terms only)

GO ID	GO term	Typea	Number of genes		P valued
			Sign.b	Ref.c
1. Direct JA treatment: significant JJ–JC and/or CJ–CC contrasts
GO:0009695	Jasmonic acid biosynthetic process	P	14	23	2.0−10
GO:0009611	Response to wounding	P	44	379	9.2−8
GO:0042401	Cellular biogenic amine biosynthetic process	P	17	78	7.0−7
GO:0006571	Tyrosine biosynthetic process	P	14	52	8.0−7
GO:0009094	l‐Phenylalanine biosynthetic process	P	14	52	8.0−7
GO:0000162	Tryptophan biosynthetic process	P	15	63	1.2−6
GO:0072329	Monocarboxylic acid catabolic process	P	12	44	4.4−6
GO:0009423	Chorismate biosynthetic process	P	4	1	1.8−5
GO:0006635	Fatty acid beta‐oxidation	P	9	27	1.9−5
GO:0051707	Response to other organism	P	92	1291	3.6−5
GO:0050660	Flavin adenine dinucleotide binding	F	9	31	4.6−5
GO:0009821	Alkaloid biosynthetic process	P	6	11	5.7−5
GO:0005783	Endoplasmic reticulum	C	51	609	7.9−5
GO:0080167	Response to karrikin	P	29	294	2.6−4
GO:0004190	Aspartic‐type endopeptidase activity	F	6	16	2.9−4
GO:0008970	Phosphatidylcholine 1‐acylhydrolase activity	F	3	1	3.3−4
GO:0052572	Response to host immune response	P	6	17	3.7−4
GO:0034976	Response to endoplasmic reticulum stress	P	6	17	3.7−4
GO:0052033	Pathogen‐associated molecular pattern dependent induction by symbiont of host innate immune response	P	6	17	3.7−4
GO:0030433	ER‐associated ubiquitin‐dependent protein catabolic process	P	4	5	3.9−4
GO:0005777	Peroxisome	C	29	304	5.5−4
GO:0009415	Response to water	P	40	482	6.2−4
GO:0001676	Long‐chain fatty acid metabolic process	P	4	6	6.3−4
GO:0009753	Response to jasmonic acid	P	31	336	6.3−4
2. Parental JA treatment: significant JJ–CJ and/or JC–CC contrasts
No significant enrichment of GO terms detected

For this GO enrichment analysis, genes were considered to be differentially expressed at an FDR = 0.20 significance threshold.

^aC, cellular component; F, molecular function; P, biological process.

^bSignificant gene set for direct JA effect: 1519 significant contigs at FDR 0.20 = 664 putative genes, 526 of which with GO annotation were included in the enrichment analysis. Significant gene set for parental JA effect: 451 significant contigs at FDR 0.20 = 173 putative genes, 133 of which with GO annotation were included in the enrichment analysis.

^cReference gene set consists of 11 961 analyzed and GO‐annotated putative genes.

^dTwo‐sided Fisher's exact test; all P‐values are significant after FDR control at 0.05.