The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information

doi:10.1186/1741-7007-5-1

BMC Biology

Volume 5

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Methodology article

The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information

Naoki Irie and Atsuko Sehara-Fujisawa

Department of Growth Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kawahara-cho 53, Shogo-in, Kyoto 606-8507, Japan

author email corresponding author email

BMC Biology 2007, 5:1doi:10.1186/1741-7007-5-1


Published:	12 January 2007

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Additional File 1:

Taxonomic classification of homologues of mouse protein-coding genes according to taxonomic range. A: Taxonomic classification of mouse genome. B: Taxonomic classification of mouse developmental genes (see Methods for the definition of developmental genes). Classifications were defined by mouse homologues found in no other organisms (M. musculus only), those shared with R. norvegicus (Rodent); with Homo sapiens, Canis familiaris or Bos taurus (Mammal, but not Rodent); with Gallus gallus (Aves, but not Mammal); with Xenopus tropicalis (Amphibians, but not Aves); with Danio rerio, Takifugu rubripes or Tetraodon nigroviridis (Teleosts, but not Amphibians); with Ciona intestinalis (Ciona, but not Teleosts); with Drosophila melanogaster, Anopheles gambiae, Apis mellifera or Caenorhabditis elegans (Protostomes, but not Ciona); or with Saccharomyces cerevisiae (Yeast, but not Protostomes).

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Mutant phenotypes of vertebrate developmental genes expressed at the phylotypic stage. Within 254 vertebrate developmental genes expressed at stages 14 or 15 (see Table 1 for staging), 159 ENSEMBL genes were associated with mutant mouse information at Mouse Genome Informatics [29]. The number of ENSEMBL genes linked to each Mammalian Phenotype ID is shown. MP, mammalian phenotype

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Additional File 3:

Ancestor indexes obtained for genes expressed during Ciona intestinalis embryogenesis. A: EST libraries used to evaluate the ancestor indexes of genes expressed during C. intestinalis embryogenesis. Each stage contained on average 58,171 EST counts (43,912–98,568), which corresponded to 2,571 (2,156–3,098) non-redundant ENSEMBL C. intestinalis genes. B: Bilaterian ancestor indexes calculated for C. intestinalis embryogenesis (14,278 genes). Bilaterian genes were defined by at least one Ciona homologue present in protostomes (see Fig. 1 for genome datasets). L: non-redundant gene expression profile of late stages (larval and young adult). EST, expressed sequence tag; dbEST, database EST; E, embryonic day.

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