This result contrasts with the good performance of cellular categories, notably the 'Posttranslational modification, protein turnover, chaperones' (O) and 'Cell motility and secretion' (N) categories.
These response pathways included cellular categories derived from KEGG, GO, TRANSPATH and TRANSFAC, plant-specific response pathways described in MapMan [ 6] and an individually assembled category named "metal homeostasis".
This analysis indicated that the incorporation of plant-specific physiological categories into GSEA added possibilities for novel physiological interpretations at whole organism level that were not achieved by merely concentrating on cellular categories.
Furthermore, amino acid biosynthesis, replication, transcription, and the cell envelope were well represented compared with other cellular categories such as the biosynthesis of cofactors, cellular processes, purines, and pyrimidines.
Skeletal muscle regeneration is a complex phenomenon that involves many regulatory processes that require a close collaboration of two major cellular categories: stem/progenitor cells and surrounding supporting interstitial cells.
Among the top molecular and cellular categories, we observed the presence of the most common functions related to EGF signaling such as cell death, cell growth and proliferation [ 1], being cancer the top disease.
Due to the diversity and little overlap of cellular categories hit in between the different comparisons we were not able to represent the results in Venn diagrams in any reasonable manner (not shown).
In the GO study, we identified 54 biological process categories, 24 cellular component categories and 18 molecular function categories.
Of the functional categories tested, 10 Cellular Component categories, 20 Biological Process categories and 12 Molecular Function categories showed significant deviations from expected equal proportions of high, intermediate and low divergence categories at the Bonferroni-adjusted α level.
