RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects.
RNA interference (RNAi) is being used in large-scale genomic studies as a rapid way to obtain in vivo functional information associated with specific genes. How best to archive and mine the complex data derived from these studies provides a series of challenges associated with both the methods used to elicit the RNAi response and the functional data gathered. RNAiDB (RNAi Database; http://www. rnai.org) has been created for the archival, distribution and analysis of phenotypic data from large-scale RNAi analyses in Caenorhabditis elegans. The database contains a compendium of publicly available data and provides information on experimental methods and phenotypic results, including raw data in the form of images and streaming time-lapse movies. Phenotypic summaries together with graphical displays of RNAi to gene mappings allow quick intuitive comparison of results from different RNAi assays and visualization of the gene product(s) potentially inhibited by each RNAi experiment based on multiple sequence analysis methods. RNAiDB can be searched using combinatorial queries and using the novel tool PhenoBlast, which ranks genes according to their overall phenotypic similarity. RNAiDB could serve as a model database for distributing and navigating in vivo functional information from large-scale systematic phenotypic analyses in different organisms.
Gunsalus
Kristin C
KC
Center for Comparative Functional Genomics, Department of Biology, New York University, 1009 Silver Building, 100 Washington Square E., New York, NY 10003, USA. kcg1@nyu.edu
Yueh
Wan-Chen
WC
MacMenamin
Philip
P
Piano
Fabio
F
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000502:physiology*; D016208:Databases, Factual; D015536:Down-Regulation; D016678:Genome; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D010641:Phenotype; D034622:RNA Interference; D012984:Software