Gene Set Enrichment Analysis (version 2.0.13) (Subramanian et al., 2005) was used to identify biological terms, pathways, and processes that were coordinately up- or down-regulated with senescence.
GSEA was used to identify biological terms, pathways, and processes that were overrepresented among the genes that were up- or down-regulated with respect to various pairwise comparisons.
It provides a collection of well-defined biological terms, spanning biological processes, molecular functions and cellular components.
To examine the functional interplay of proteins in more detail, the individual proteins were annotated with gene ontology (GO) biological process terms and the major associated processes were examined (Appendix Table S15).
Pollination shares striking similarities with fungal infection in terms of biological responses and processes that result in cell death [ 27, 28].
The GO database (http://www.geneontology.org) was used for analysis of associated GO terms and biological processes [28].
To evaluate the biological relevance of the 49 comodules, we calculated their enrichment in GO biological process terms and KEGG pathways using the hypergeometric test.
Among them, there were 15,576 proteins annotated with molecular function terms, 14,911 proteins annotated with biological process terms, and 16,983 proteins annotated with cellular component terms.
This high similarity is consistent with the up-regulated GO biological process terms and gene expression profiles as described earlier.
Significantly enriched Gene Ontology biological process terms and KEGG pathway terms were detected for 343 and 60 modules, respectively.
