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New genes in the evolution of the neural crest differentiation program

Juan-Ramon Martinez-Morales*, Thorsten Henrich, Mirana Ramialison and Joachim Wittbrodt*

Author Affiliations

Developmental Biology Unit, EMBL, Meyerhofstra├če, 69117 Heidelberg, Germany

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Genome Biology 2007, 8:R36  doi:10.1186/gb-2007-8-3-r36

Published: 12 March 2007

Additional files

Additional data file 1:

The table includes a full list of the statistically over-represented GO annotations of genes belonging to each of the seven categories (cutoff P < 0.001, sample count = 15).

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Open Data

Additional data file 2:

The table comprises a full list of the 615 neural crest genes compiled using Phenotype Ontology annotations for each of the seven temporal categories considered in this work: prokaryota (pro), eukaryota (euk), metazoa (met), deuterostomia (deu), chordata (cor), vertebrata (ver), and mammalia (mam).

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Open Data

Additional data file 3:

The table shows statistically over-represented GO annotations of the set of neural crest developmental genes that emerged in vertebrates (cutoff P < 0.001).

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Open Data

Additional data file 4:

ClustalX alignment of mouse neurotropins against the echinoderm peptide. The comparison reveals a limited amino acid identity.

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Open Data

Additional data file 5:

Phylogenetic analysis of neural crest Pfam domains emergence through evolution. The table shows a full list of the compiled 615 genes involved in neural crest development and the first appearance of their Pfam domains in the different clades. All the corresponding Pfam domains of these genes, when these domains have appeared, and the classification of the genes according to our previous sequential blast analysis (blast; color-coded) are indicated.

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Open Data

Additional data file 6:

A complete list of genomes of species included in this work and their respective source is compiled in this table. Abbreviations: arc (archaeobacteria), bac (bacteria), euk (eukaryota), met (metazoa), deu (deuterostomia), cor (chordata), ver (vertebrata).

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Open Data

Additional data file 7:

As a control of our gene phylogeny analysis, we also run the sequential blast pipeline using other vertebrate groups, namely (chicken, xenopus and zebrafish genomes). The tables show the number or percentage of genes assigned to each evolutionary category. The graphical representation of the gene phylogeny for the four vertebrate species analyzed revealed a very similar gene loss/emergence profile.

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Open Data