Table I. Overrepresented GO terms in the set of up-regulated genes in the SPMS overexpressing line 35S::SPMS-9

Genes called up-regulated by the significance analysis of microarrays and associated to GO terms were used to perform a GO overrepresentation analysis using Ontologizer software with settings Term-For-Term/Westfall-Young-Single-Step. A total of 22,766 genes were in the population set, 443 of which were in the study set. Overrepresented GO categories (adjusted P value ≤ 0.05) are listed.

GO IDaNamebNSPcStudy CountdPopulation CounteAdjusted P Valuef
GO:0050896Response to stimulusB1332758<1.0 × 10−300
GO:0006952Defense responseB51586<1.0 × 10−300
GO:0006950Response to stressB841,571<1.0 × 10−300
GO:0010200Response to chitinB23116<1.0 × 10−300
GO:0010033Response to organic substanceB62966<1.0 × 10−300
GO:0042221Response to chemical stimulusB741,377<1.0 × 10−300
GO:0009743Response to carbohydrate stimulusB24180<1.0 × 10−300
GO:0042742Defense response to bacteriumB18132<1.0 × 10−300
GO:0009719Response to endogenous stimulusB43768<1.0 × 10−300
GO:0009617Response to bacteriumB20187<1.0 × 10−300
GO:0002376Immune system processB19173<1.0 × 10−300
GO:0006955Immune responseB19173<1.0 × 10−300
GO:0051707Response to other organismB31461<1.0 × 10−300
GO:0009753Response to jasmonic acid stimulusB17142<1.0 × 10−300
GO:0009607Response to biotic stimulusB31478<1.0 × 10−300
GO:0045087Innate immune responseB16157<1.0 × 10−300
GO:0051704Multiorganism processB31570<1.0 × 10−300
GO:0016740Transferase activityF792,390<1.0 × 10−300
GO:0051716Cellular response to stimulusB29579<1.0 × 10−300
GO:0009605Response to external stimulusB19294<1.0 × 10−300
GO:0009816Defense response to bacterium, incompatible interactionB626<1.0 × 10−300
GO:0009725Response to hormone stimulusB32703<1.0 × 10−300
GO:0008219Cell deathB111090.002
GO:0016265DeathB111090.002
GO:0009814Defense response, incompatible interactionB10920.004
GO:0009611Response to woundingB121360.004
GO:0048583Regulation of response to stimulusB121400.008
GO:0009626Plant-type HRB6330.036
GO:0034050Host programmed cell death induced by symbiontB6330.036
GO:0016301Kinase activityF451,2340.038
  • a Accession number of the GO term.

  • b GO term name.

  • c Namespace or subontology (B, biological process; C, cellular component; F, molecular function).

  • d The number of genes in the study set annotated to the GO term in question.

  • e The number of genes in the population set annotated to the GO term in question.

  • f Adjusted P value.