Clone mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans.
Bottom Line: Proper interpretation of results from RNAi experiments requires a series of analytical steps, from the verification of the identity of bacterial clones, to the identification of the clones' potential targets.Despite the popularity of the technique, no user-friendly set of tools allowing these steps to be carried out accurately, automatically, and at a large scale, is currently available.We show that Clone Mapper overcomes the limitations of existing techniques and provide examples illustrating its potential for the identification of biologically relevant genes.
Affiliation: Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Case 906, 13288 Marseille Cedex 9, France INSERM U1104, 13288 Marseille, France CNRS UMR7280, 13288 Marseille, France.Show MeSH
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Mentions: To evaluate the potential impact of these differences in prediction, we compared the list of putative targets in four published data sets with those obtained with Clone Mapper. In the first screen, where just 29 clones were selected (Pukkila-Worley et al. 2014), Clone Mapper predicted the same targets as published; no novel targets with high scores were identified. In the second specific case (Ceron et al. 2007), 14 of 244 targets were not predicted by Clone Mapper since the insert sequences of the corresponding clones cannot be predicted. On the other hand, Clone Mapper identified 23 new targets with of score >1, 9 of which had a score >50 (Supporting Information, Table S1). Similar results were obtained for the two other studies (Fievet et al. 2013; Roy et al. 2014) (Table 1, Table S2, and Table S3). In all cases, the novel targets identified with Clone Mapper formed part of a closely linked network (Figure 6). The interconnectivity of the novel RNAi targets suggests that they may be functionally important for the biological process under study. Such a hypothesis requires direct experimental validation, but the results demonstrate the potential utility of Clone Mapper in gene discovery.
Affiliation: Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Case 906, 13288 Marseille Cedex 9, France INSERM U1104, 13288 Marseille, France CNRS UMR7280, 13288 Marseille, France.