International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


POSTER 10 - BIOINFORMATICS AND EXPRESSION ANALYSIS OF MOUSE CHROMOSOME 5 (0-75MB REGION)

Shao H 1, Gan T 2, Valladares O 1, Manduchi E 2, Pinney D 2, Stoeckert C 2, Bucan M 1

1Department of Genetics, University of Pennsylvania, Philadelphia, United States, 2 Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, United States

Although sequences for large eukaryotic genomes (e.g. human, mouse, rat, chicken etc) are being completed, it remains a challenge to identify all encoded genes.  Approaches used to date include ab initio gene prediction, similarity-based annotation, and direct alignment of transcribed sequences.  We are using the proximal portion of mouse Chromosome 5 and several public databases to assemble a gene index for the 75 Mb region – target for region-specific ENU mutagenesis screen.  A Database of Transcribed Sequences (DoTS, http://www.allgenes.org/) has identified over 150 novel transcripts, in addition to 550 genes annotated by the ENSEMBL and Celera databases.  Over 81 % of these transcripts were verified using a custom-built 70-mer oligo microarray hybridized with embryos cDNA (E9.5, E12.5, E14.5 and E17.5) and cDNA from several adult tissues.  The expression map of the chromosome is being assembled by integration of our array data, with expression data from large scale efforts (Hamatani et al. 2004, Su et al. 2004).  This gene index and the expression map will be used to suggest and rank candidate genes for identified embryo-lethal and behavioral mutations, as well as in disease-gene identification in the corresponding portions of the human genome.

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