Analysis of global mRNA expression profile in nub1mutants compared to wild type flies. (A) A factorial map of principal component analysis was conducted using all transcripts found to be expressed over background signal in at least one sample group. Samples are colored group-wise. The percentage found for each component in the plot can be interpreted as the variation seen within and between the different sample groups. For the principal component analysis plots, the largest explainable variance is found in component 1, where 44% of the data’s variation can be explained. This 44% is the biological difference found between the different tissues, gut or carcass. Component 2 with its 13% divides the data based on the biological variance explained by strain, that is, nub1 or wild type (wt). Component 3, with 8%, biologically nuances the data even further. (B) Venn diagram showing the overlap of carcass and gut differentially expressed genes in nub1 compared to wild type after removing background and filtering for fold change >2. (C) List of ‘Immune and Stress Response’ genes up- or down-regulated in nub1 mutants. Names and functions of the 58 genes constituting the enriched Biological Process cluster ‘Immune system and Response processes’ identified by a gene set enrichment analysis (Additional file 4) in carcass (without head and gut) from nub1 mutants. Fold change (mean values) of mRNA levels is indicated by numbers and color-coded (red, up-regulation; green, down-regulation). Genes that previously have been shown to be targets of the NF-κB/Relish/IMD pathway or a combination of NF-κB/Relish/IMD and NF-κB/Dif/Toll pathways [44–46] are indicated by ‘YES’.