Surprising complexity of the ancestral apoptosis network

doi:10.1186/gb-2007-8-10-r226

Genome Biology

Volume 8
Issue 10

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Surprising complexity of the ancestral apoptosis network

Christian M Zmasek¹^* , Qing Zhang¹^* , Yuzhen Ye² and Adam Godzik¹^,3

¹Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA

²School of Informatics, Indiana University, E.10th Street, Bloomington, IN 47408, USA

³Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, Gilman Drive, La Jolla, CA 92093, USA

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R226doi:10.1186/gb-2007-8-10-r226


Published:	24 October 2007

Subject areas: Evolution, Genome studies, Bioinformatics

Additional files

Additional data file 1:

This phylogeny was calculated using a Bayesian approach (MrBayes) based on a MAFFT alignment of Peptidase_C14 domains. Posterior probability values are shown for each branch (for detailed information, see Materials and methods). Species abbreviations: BRAFL, Branchiostoma floridae (amphioxus); BRARE, Brachydanio rerio (zebrafish); CAEBR, Caenorhabditis briggsae; CAEEL, Caenorhabditis elegans; CANFA, Canis familiaris (dog); CHICK, Gallus gallus (chicken); CIOIN, Ciona intestinalis (sea squirt); DROME, Drosophila melanogaster (fruit fly); FUGRU, Fugu rubripes (Japanese pufferfish); NEMVE, Nematostella vectensis (starlet sea anemone); STRPU, Strongylocentrotus purpuratus (purple sea urchin); TETNG, Tetraodon nigroviridis (green pufferfish); and XENTR, Xenopus tropicalis (western clawed frog). For a detailed list of protein sequences see Additional data file 4. Para-caspases are excluded from this phylogeny.

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Additional data file 2:

Protein sequences for Figure 2 (phylogeny and domain organization of CED-4/Apaf-1 homologs).

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Additional data file 3:

Protein sequences for Figure 3 (phylogeny of the multi-motif Bcl-2 family).

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Additional data file 4:

Protein sequences for Additional data file 1 (phylogeny of the caspase family).

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