title: Clone mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans.
abstract: RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a powerful method to investigate gene function. It is widely used in the Caenorhabditis elegans research community. An expanding number of laboratories conduct genome-wide RNAi screens, using standard libraries of bacterial clones each designed to produce a specific double-stranded RNA. 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 report here the design and production of Clone Mapper, an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans. We show that Clone Mapper overcomes the limitations of existing techniques and provide examples illustrating its potential for the identification of biologically relevant genes. The Clone Mapper tools are freely available via http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.
authors.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.
authors.forename: Nishant
authors.initials: N
authors.lastname: Thakur
authors.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.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pujol
authors.affiliation: Institut de Mathématiques de Marseille, Site Sud, Campus de Luminy, Case 907 13288 Marseille Cedex 9, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Tichit
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Case 906, 13288 Marseille Cedex 9, France Institut de Mathématiques de Marseille, Site Sud, Campus de Luminy, Case 907 13288 Marseille Cedex 9, France CNRS UMR7280, 13288 Marseille, France ewbank@ciml.univ-mrs.fr.
authors.forename: Jonathan J
authors.identifier: http://orcid.org/0000-0002-1257-6862
authors.initials: JJ
authors.lastname: Ewbank
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D008969:Molecular Sequence Data; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D012984:Software
chemical_list: D034741:RNA, Small Interfering
keywords: MPscan; algorithm; database; functional genomics; gene discovery