Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction

Table 1 GO statistical analysis for analyzing transcript sequences

Node	Term	Genes outside node	Genes in node	Significant	p value
GO:0055114	Oxidation-reduction process	1085	116	108	8.26E-005
GO:0006979	Response to oxidative stress	1127	74	63	0.0015
GO:0005975	Carbohydrate metabolic process	1090	111	61	0.0804
GO:0042538	Hyperosmotic salinity response	1184	17	17	0.0008
GO:0009414	Response to water deprivation	1172	29	13	0.0049
GO:0007010	Cytoskeleton organization	1148	53	8	0.0032
GO:0009813	Flavonoid biosynthetic process	1177	24	7	0.0029
GO:0009807	Lignan biosynthetic process	1195	6	6	0.0133
GO:0009266	Response to temperature stimulus	1122	79	6	0.0406
GO:0046274	Lignin catabolic process	1195	6	6	0.0675
GO:0009718	Anthocyanin biosynthetic process	1191	10	5	0.0006
GO:0009627	Systemic acquired resistance	1194	7	5	0.0073
GO:0000165	MAPK cascade	1196	5	5	0.0091
GO:0009741	Response to brassinosteroid stimulus	1195	6	5	0.0302
GO:0009699	Phenylpropanoid biosynthetic process	1165	36	3	9.85E-005
GO:0009850	Auxin metabolic process	1196	5	3	0.0154
GO:0000272	Polysaccharide catabolic process	1181	20	3	0.0485
GO:0009698	Phenylpropanoid metabolic process	1155	46	2	9.93E-005
GO:0009808	Lignin metabolic process	1185	16	2	0.01864
GO:0009938	Negative regulation of gibberellic acid mediated signaling pathway	1199	2	2	0.0624
GO:0009851	Auxin biosynthetic process	1199	2	1	0.0154
GO:0009861	Jasmonic acid and ethylene-dependent systemic resistance	1200	1	1	0.0749

Gene Ontology (GO) terms identified to be enriched or depleted according to the comparison of the distribution of the gene-associated Log2FC among all differentially expressed genes classified in the GO category “biological process”. The value of Log2FC obtained by differential expression analysis (at p-value < =0.1) was used as the measure of choice to rank genes as “differentially expressed” or “not differentially expressed”. Then a Wilcoxon-rank test was performed with 1201 genes to compare the ranks of the genes in the tested GO term (Genes in node) with the ranks of the remaining genes in the top category (Genes not in node). For each comparison a p-value was obtained and a cut-off provided as the global test statistic to gauge the significance of the complete data set was used to establish the number of genes with relevant associations with each tested category (Significant).

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