EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes

We have developed an integrated database that is specialized for the study of imprinted disease genes. The database contains novel candidate imprinted genes identified by the RIKEN full-length mouse cDNA microarray study, information on validated single nucleotide polymorphisms (SNPs) to confirm imprinting using reciprocal mouse crosses and the predicted physical position of imprinting-related disease loci in the mouse and human genomes. It has two user-friendly search interfaces: the SNP-central view (MuSCAT: MoUse SNP CATalog) and the candidate gene-central view (CITE: Candidate Imprinted Transcripts by Expression). The database, EICO (Expression-based Imprint Candidate Organizer), can be accessed via the World Wide Web (http://fantom2.gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits.

[1]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[2]  Jun Kawai,et al.  Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. , 2002, Biochemical and biophysical research communications.

[3]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[4]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[5]  M. Tomita,et al.  Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. , 2003, Genome research.

[6]  W. Reik,et al.  Genomic imprinting: parental influence on the genome , 2001, Nature Reviews Genetics.

[7]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[8]  J. Mullikin,et al.  SSAHA: a fast search method for large DNA databases. , 2001, Genome research.

[9]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[10]  Yoshihide Hayashizaki,et al.  [FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones]. , 2003, Seikagaku. The Journal of Japanese Biochemical Society.

[11]  Hideo Matsuda,et al.  Development and evaluation of an automated annotation pipeline and cDNA annotation system. , 2003, Genome research.

[12]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[13]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..

[14]  Yoshihide Hayashizaki,et al.  Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. , 2003, Genome research.

[15]  Yoshihide Hayashizaki,et al.  Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. , 2003, Genome research.