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This article is part of the supplement: Proceedings of the 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology (X-meeting 2009)

Open Access Proceedings

The role of exon shuffling in shaping protein-protein interaction networks

Douglas V Cancherini1, Gustavo S França12 and Sandro J de Souza1*

Author Affiliations

1 Ludwig Institute for Cancer Research, São Paulo Branch, Brazil

2 Ph. D. Program, Department of Biochemistry, Institute of Chemistry, University of São Paulo, Brazil

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BMC Genomics 2010, 11(Suppl 5):S11  doi:10.1186/1471-2164-11-S5-S11

Published: 22 December 2010

Additional files

Additional file 1:

Influence of shuffling upon presence in PPI networks in selected species. Percentage of protein-coding genes in PPI networks according to shuffling profile category in mouse, worm, fly, fungus, and plant species (bar charts), and chi-square values and p-values for comparisons among shuffling profile groups concerning presence in PPI networks (tables). Numbers above bars indicate the absolute number of genes in the corresponding PPI network, and the total number of protein-coding genes of the species.

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Additional file 2:

Vertex degree in PPI networks according to shuffling profile category for selected species. Data come from the following species: human (A/E), mouse (F and B/G), D. melanogaster (H and C/I), C. elegans (J and D/K), C. neoformans (L), and A. thaliana (M). Boxplots and tables display, respectively, vertex degree distributions and p-values for group comparisons. Tables F, H, J, L, and M make use of all genes in PPI network, and present the results of statistical analyses concerning main text figures 3B, 3C, 3D, 3E and 3F, respectively. In contrast, boxplot/table pairs A/E, B/G, C/I, and D/K consider genes in PPI network after a paralog confluence procedure for vertices in order to control for the effect of gene duplications. In boxplots, X and O indicate arithmetic and geometric mean, respectively, whiskers mark percentiles 10 and 90, and protein length for each group is reported as mean ± standard deviation.

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Additional file 3:

Vertex degree in PPI networks for genes with and without paralogs. In boxplots of vertex degree, analyzed species were human (A), mouse (B), D. melanogaster (C), C. elegans (D), C. neoformans (E), and A. thaliana (F). In metazoan species (A to D), genes of the ES subsets were previously excluded. Estimated p-values for group comparisons are found in tables G (human and mouse), H (fly and worm) and I (fungus and plant). In boxplots, X and O indicate arithmetic and geometric mean, respectively, whiskers mark percentiles 10 and 90, and protein length for each group is reported as mean ± standard deviation.

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Additional file 4:

Self-interactions according to shuffling profile category in human. Percentages and explicit fractions of self-interacting vertices, for the human PPI network subjected to a paralog confluence procedure, are seen in part 4A, whereas chi-square values and p-values regarding comparisons among groups are shown in part 4B.

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