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The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

John W Whitaker, Glenn A McConkey and David R Westhead*

Author Affiliations

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK

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Genome Biology 2009, 10:R36  doi:10.1186/gb-2009-10-4-r36

Published: 15 April 2009

Additional files

Additional data file 1:

Details of the organism groups and PHAT selection statements used to identify the putative gene transfers.

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Additional data file 2:

The table shows all of the enzymes that are predicted as being present in each of the organism groups. Enzymes that are not predicted as being gene transfers are shown in orange, EGT enzymes are shown in green, HGT enzymes are shown in blue and double transfers are shown in yellow. The enzymes are grouped by KEGG pathway.

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Additional data file 3:

For each organism group and gene transfer type (EGT and HGT) the following information is given: the number of enzymes predicted as being gene transfers; the number of these enzymes present within the KEGG metabolic network; the average number of connections between the nodes within the KEGG metabolic network; the average number of connection between the same number of enzymes calculated over 10,000 random samples; a P-value and a Z score based on these random samples. Then, for each of the gene transfer types, t-tests and Wilcoxon signed-rank tests are given to calculate the probability that the transfers are more connected than random over all the species groups.

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Additional data file 4:

The EGT enrichment analysis for map groups, KEGG maps, KEGG modules, EC number and co-factors is given. For map groups and the first EC number tier both over- and under-representation are shown and for all other enrichment analysis only over-representation is shown. For all enrichment types the following information is given: the number of EGT enzymes of that type for the given organism; the total number of enzymes of that type from the given organism; a P-value corresponding to the probability of the level of representation; and an enrichment score. The P-values were calculated using the hypergeometric distribution. For KEGG modules the number of additional low confidence EGT predictions is also shown. The low-confidence predictions lack the bootstrap support and manual inspection that the high-confidence predictions have.

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Additional data file 5:

The same as Additional data file 4 except showing other HGTs.

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Additional data file 6:

LPS biosynthesis enzymes that had hits to either Phytophthora genomes are listed. Next to the E. coli enzyme name is the KEGG ortholog group ID and the EC number of the group. The E-value of the hit in each of the genomes is listed.

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