Denoising inferred functional association networks obtained by gene fusion analysis

doi:10.1186/1471-2164-8-460

BMC Genomics

Volume 8

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Kamburov A
Goldovsky L
Freilich S
Kapazoglou A
Kunin V
Enright AJ
Tsaftaris A
Ouzounis CA

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Kamburov A
Goldovsky L
Freilich S
Kapazoglou A
Kunin V
Enright AJ
Tsaftaris A
Ouzounis CA
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Research article

Denoising inferred functional association networks obtained by gene fusion analysis

Atanas Kamburov¹^,5 , Leon Goldovsky¹^,2^,3 , Shiri Freilich¹^,2^,3 , Aliki Kapazoglou³ , Victor Kunin¹^,6 , Anton J Enright⁴ , Athanasios Tsaftaris³ and Christos A Ouzounis¹^,2^,3^,7

¹Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK

²Computational Genomics Unit at the Center for Research & Technology Hellas, GR-57001 Thessalonica, Greece

³Institute of Agrobiotechnology, Center for Research & Technology Hellas, GR-57001 Thessalonica, Greece

⁴The Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK

⁵Max-Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany

⁶DOE Joint Genome Institute, 2800 Mitchel Drive, Walnut Creek CA 94598, USA

⁷Centre for Bioinformatics, School of Physical Sciences and Engineering, King's College London, Strand, London WC2R 2LS, UK

author email corresponding author email

BMC Genomics 2007, 8:460doi:10.1186/1471-2164-8-460


Published:	14 December 2007

Additional files

Additional File 1:

Dependence of fraction of composite (fused) genes on genome size. The x-axis represents genome size (number of genes) for a given query species, the y-axis represents the fraction of composite genes in that species. Color coding as in Figure 3.

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Additional File 2:

a) Dependence of fraction of composite (fused) genes on fraction of component (un-fused) genes, as a ratio of unique instances over total number of genes, per genome. b) Distribution of fraction of distinct interacting proteins in the three domains of life (color coding as in Figure 3) and all domains (grey).

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Additional File 3:

Distribution of slopes (relative rank order of reference species and number of contributed interactions) across genomes (see Figure 3c for an example). a) Distribution of slope values for all species; 25 species are excluded with slopes>12. b) Plot of slopes versus genome size. The x-axis represents the slope for a given species, the y-axis represents genome size (total number of genes) for that species. Both axes are shown on a logarithmic scale. Grey boxes represent the 25 species with slopes>12.

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Additional File 4:

Distribution of composites across 184 genomes.

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Additional File 5:

Distribution of interactions across 184 genomes.

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Additional File 6:

Analysis of predicted interactions from Chlamydia trachomatis. Examples of previously characterised interactions in C. trachomatis that are detected by gene fusion analysis. Cases in bold are presumed as known; cases in purple are artifacts from genomic paralogy.

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Additional File 7:

Examples of predicted interactions from Arabidopsis thaliana. The species of origin is also given for the composite proteins.

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Additional File 8:

Inferred interactions in this study. The data forms part of the COGENT++ data environment.[36].

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