The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

doi:10.1186/1471-2148-8-23

BMC Evolutionary Biology

Volume 8

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Research article

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

Wagied Davids¹ and Zhaolei Zhang¹^,2

¹Banting & Best Department of Medical Research (BBDMR), Donnelly Centre for Cellular & Biomolecular Research (CCBR), University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada

²Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada

author email corresponding author email

BMC Evolutionary Biology 2008, 8:23doi:10.1186/1471-2148-8-23


Published:	24 January 2008

Additional files

Additional file 1:

Comparison between different HFT gene detection methods. (A) This is a 4-way comparison Venn diagram illustrating the intersection and differences between various horizontal gene transfer detection methods investigated. The comparison included a non-surrogate phylogeny and gene presence/absence based method developed by Price [15] versus three surrogate methods which included HGT-DB [27], the method published by Mrazek and Karlin [28] and a support vector machine-based method (HGT_SVM) developed by Tsirigos and Rigoutsos [29]. (B): This is a comparison of Cluster of Orthologous Group (COG) functional categories between Core, Non-core and HGT gene sets obtained using various methods of horizontal gene transfer detection. The comparison included a non-surrogate phylogeny and gene presence/absence based method developed by Price [15] versus three surrogate methods which included HGT-DB [27], the method published by Mrazek and Karlin [28] and a support vector machine-based method (HGT_SVM) developed by Tsirigos and Rigoutsos[29].

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Additional file 2:

Codon usages between core, Non-core and HGT genes. This is a correspondence analysis of codon usage from E. coli Core, Non-core, and putative HGT genes using the first two principal components.

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Additional file 3:

Comparison between two E. coli interaction studies. This is a comparison of COG functional classes between Arifuzzaman et al. (2006) and Butland et al (2005) E. coli protein interaction networks.

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Additional file 4:

Comparison between two E. coli interaction studies. This is a comparison between Arifuzzaman et al. (2006) and Butland et al. (2005) published protein interaction data sets.

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Additional file 5:

Statistical tests for the COG distribution. (A) Kruskal-Wallis ANOVA with Scheirer-Ray-Hare extension on the ranks of COG category counts in the Genome. (B) Kruskal-Wallis ANOVA with Scheirer-Ray-Hare extension on the ranks of COG category counts in the Operons. (C) Kruskal-Wallis ANOVA with Scheirer-Ray-Hare extension on the ranks of COG category counts in the protein interaction network (PPI).