Open access to the FANTOM (Functional ANnoTation Of Mouse)

Hidemasa Bono1, Takeya Kasukawa1, Itoshi Nikaido1, Hideo Matsuda2, Yasushi Okazaki1, and Yoshihide Hayashizaki1

1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama, Japan 2Department of Informatics and Mathematical Science, Graduate School of Engineering Science, Osaka University, Japan

The RIKEN Mouse Gene Encyclopedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs(cDNA) and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analyzed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs revealed new members of known gene families and identified new families (Nature, 409, 685-690(2001)).The experts from genomics and bioinformatics, including well-trained MGI (Mouse Genome Informatics) annotators extensively and substantially worked for these functional annotations. In that meeting, web-based system called FANTOM+ was used to annotate functional information for all these cDNAs.
Interactive viewer for browsing these annotations and the evidence for these, which is a subset of FANTOM+ system, is now opened to the public. All functional annotation of cDNA clones are formatted as XML, called MaXML(Mouse Annotation XML), in order to share them in the research community for non-interactive, bulk genome analysis in silico. Because these annotations and evidences for them are updated frequently, dynamic access to the annotation itself is really on demand for biological study. To deal with such demand, we are working on the implementation of parser for MaXML and network-based system for distributing these annotations. We will report the current status of our project.