BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

BodyMap-Xs () is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically.

[1]  Damian Smedley,et al.  Ensembl 2005 , 2004, Nucleic Acids Res..

[2]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[3]  K. H. Wolfe,et al.  Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. , 2004, Genome Research.

[4]  C. V. Jongeneel,et al.  eVOC: a controlled vocabulary for unifying gene expression data. , 2003, Genome research.

[5]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[6]  Teruyoshi Hishiki,et al.  The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms , 2004, Nucleic Acids Res..

[7]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[8]  Minoru Kanehisa,et al.  Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags , 2002, Nucleic Acids Res..

[9]  Martin J. Lercher,et al.  Clustering of housekeeping genes provides a unified model of gene order in the human genome , 2002, Nature Genetics.

[10]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[11]  Gene W. Yeo,et al.  Variation in alternative splicing across human tissues , 2004, Genome Biology.

[12]  Kohei Suzuki,et al.  PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries , 2004, Nucleic Acids Res..

[13]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[14]  Christopher J. Lee,et al.  Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.

[15]  Cristian I. Castillo-Davis,et al.  cis-Regulatory and protein evolution in orthologous and duplicate genes. , 2004, Genome research.

[16]  Greg Elgar,et al.  Fugu ESTs: new resources for transcription analysis and genome annotation. , 2003, Genome research.

[17]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[18]  Teruyoshi Hishiki,et al.  BodyMap: a human and mouse gene expression database , 2000, Nucleic Acids Res..

[19]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology , 2003, Nucleic Acids Res..

[20]  Gregory D. Schuler,et al.  ESTablishing a human transcript map , 1995, Nature Genetics.

[21]  R. Fleischmann,et al.  Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. , 1995, Nature.

[22]  Paul E. Boardman,et al.  A Comprehensive Collection of Chicken cDNAs , 2002, Current Biology.

[23]  Kousaku Okubo,et al.  Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression , 1992, Nature Genetics.