Lejeune et al. BMC Genomics 2012, 13:91 http://www.biomedcentral.com/1471-2164/13/91 Page 5 of 14 Figure 1 Reduction of YFP expression in 128Q;rff-3 nematodes treated with RNAi against GFP. Following incubation of ID447 L1 larvae with bacteria expressing either empty vector (pL4440) or RNAi against GFP (pL4417) until F1 young adults are produced, YFP levels in PLM touch receptor cells were measured by image analysis, and YFP mRNA levels were measured by qRT-PCR from whole animals. (A) Representative image showing YFP expression (pseudocolored in green) in animals treated with empty vector. The name of the mec-7p target cells is indicated. The insert shows a closer view of the left (PLMl) and right (PLMr) PLM cell. (B) Representative image showing reduced YFP expression in animals treated with RNAi against GFP. The yellow arrow indicates natural auto-fluorescence of the gut granules. This fluorescence is also present in the control animals and works as an internal control of light intensity, showing that pictures were collected in the confocal microscope under the same conditions. The insert shows a closer view of PLM cell left (PLMl) and right (PLMr). (C) YFP mRNA levels are reduced by treatment with pL4417. Data are means ± SE (n = 5). ***P < 0.001 compared to pL4440. (D) YFP expression levels in PLM cells are reduced by treatment with pL4417. Data are means ± SEM (n = 3) as compiled from greater than 70 animals/experiment. ***P < 0.001 compared to pL4440. Scale bar is 100 μm in all panels. neuron dysfunction might also modify neuronal dys- function in 19Q;rrf-3 nematodes by testing a subset of the 662 genes (245 genes choosen at random). Only 15/ 245 genes (6.1%) were found to modulate neuronal dys- function in 19Q;rrf-3 nematodes when knocked-down by RNAi (Additional file 5: Table S4), suggesting that most of the 662 genes emphasized by screens in 128Q; rrf-3 nematodes specifically modify 128Q cytotoxicity. Genome-wide RNAi screens previously aimed at identi- fying modifiers of polyQ aggregation in C. elegans [40,41], Consistent with the notion that aggregation and cytotoxicity can be genetically uncoupled [41], the over- lap with our RNAi screen was small with 12 modifiers of 128Q-neuron dysfunction previously found to enhance the aggregation of 35Q-peptides when knocked-down by RNAi [40] and three other modifiers of 128Q-neuron dysfunction previously found to sup- press the aggregation of 35Q-peptides when knocked- down by RNAi [41] (Additional file 6: Table S5). In-depth data analysis emphasizes modifiers of 128Q- neuron dysfunction in pathways associated with metabolism, development, survival and neurodegenerative disease The 662 genes associated with the modification of 128Q-neuron dysfunction appeared to encompass a vari- ety of biological processes (cell death, protein folding, intracellular transport, metabolic processes, response to stress, stress-activated pathways) that may have a role in neurodegenerative disease pathogenesis as suggested by their functional classification using GO annotations (Fig- ure 3, Additional file 7: Tables S6; Additional file 8: Table S7). To further assess the biological content cor- responding to modifiers of 128Q-neuron dysfunction, we performed two types of analysis. First, we used gene lists describing major signaling pathways (see Materials and Methods) to perform gene set enrichment analyses. This analysis was performed for genes that either aggra- vate (herein referred to as ‘protection-associated’ or PA