Each tile of the mosaic represents an individual SOM cluster and is colour-coded to represent over- and under-expression of the genes in a cluster, thus identifying the underlying gene pattern (Eichler et al, 2003).
We used the pipeline for GO enrichment analysis of CNVs in Nguyen et al. [22]; the likelihood that a GO annotation is over- or under- represented among CNVs is estimated using the hypergeometric distribution, and then the false discovery rate (FDR) is controlled (here it was kept at 5%) to select the most significant results.
Using a functional enrichment analysis of genes (see supplemental files: Tables S2, S3, S4, S5, S6, S7) it was possible to individuate statistically significant functional categories that are over- or under- represented in the differentially expressed gene-lists of the efflux pump s -deleted mutant strains described in this work in respump s -deletedd-type.
GO Terms that were over- or under- represented in the genes modulated during normal carpel development and fruit set (TIME), with respect to the rest of the array.
In the first approach we identified a number of GO slim categories that were significantly over- or under- represented in comparisons made between the sample groups.
Only significantly (z-score, p < 0.01) over/under represented TF families in each subset are shown in Figure 7, however if one family is significantly over- or under- represented at p < 0.01 in rice or Arabidopsis, and it is significant at p < 0.02 in the other species, it was indicated with a + in the latter (Additional file 2, Table S7).
General patterns of distribution were similar between organisms, with limited exceptions where particular GO slim categories were over- or under- represented in the B. terrestris unique sequences (Table 2).
Genes mainly involved in the synthesis and degradation of amino acid, cell wall, hormones, lipids, isoprenoids and ion transport, and also different transcription factors were significantly over- or under- represented in those three clusters (Additional file 13: Figure S8).
Those sets are endowed with some "collective status" described by variables S g A and S g I, assuming that regulation works in a cooperative way: hence, the collective state of a set of regulators is over- (resp. under-) represented if and only if all elements in the set share the same status.
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This type of weighting is used to protect against inspection samples which might under-represent or over-represent one or more of the SIMD categories in the population.
