Alkamide-Regulated Transcriptional Networks Figure 2. Functional classification of Arabidopsis genes differentially expressed in response to N-isobutyl decanamide treatment. Categorization of 1,281 genes regulated by treatment was obtained according to the Munich Information Center for Protein Sequences classification (MIPS) classification using FunCat database (http://mips.helmholtz-muenchen.de/proj/funcatDB/) and Arabidopsis annotation. Statistically significant categories were identified by using a hypergeometric method and Bonferroni correction with a cutoff of p-value .0.05 (A). MIPS defense-related subcategories significantly represented (B). Percentages relate to total differentially regulated genes per sampled times. The average transcriptional change of all induced genes in overrepresented functional categories was also calculated along time of treatment (C). doi:10.1371/journal.pone.0027251.g002 At5g47220), VEGETATIVE STORAGE PROTEIN2 (VSP2, At5g24770), LIPID TRANSFER PROTEINS (LTP3, LTP2 and LTP, At5g59320, At2g38530, and At4g12490, respectively) and the SENESCENCE-ASSOCIATED GENE13 (SAG13, At2g29350) sustained high expression values through our temporal kinetic experiment. The genes CORI1 (At1g19670), JAZ8 (At1g30135), ERF4 (At3g15210) and PHYTOALEXINE DEFICIENT3 (PAD3, At3g26830) showed increased expression from basal levels to induced expression levels. Four PLANT DEFENSIN genes PDF1.2a, PDF1.1, PDF1.2b and PDF1.2c (At5g44420, At1g75830, At2g26020, At5g44430) and a chitinase (BASIC CHITINASE, At3g12500) ranged from repression to induction values (Figure 4B). However, all of them, in a similar way to the genes of the JA biosynthetic pathway, were overexpressed at day 7 after alkamide treatment (Figure 4A &B). To determine whether increase in the transcript level of JA- related genes correlated with changes in endogenous levels of JA, we quantified, by gas chromatography coupled to mass spectrom- PLoS ONE | www.plosone.org 5 November 2011 | Volume 6 | Issue 11 | e27251