Methodology article
Identifying metabolic enzymes with multiple types of association evidence
1 Department of Genetics, New Research Building (NRB) Room 238, 77 Ave. Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
2 Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, 1150 St. Nicholas Ave., New York, NY 10032, USA
3 Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive 0404, Room 4126, La Jolla, CA 92093, USA
BMC Bioinformatics 2006, 7:177 doi:10.1186/1471-2105-7-177
Published: 29 March 2006Additional files
Additional File 1:
Performance of different profile similarity measures.
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Additional File 2:
Distribution of the number of orthologs per organism.
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Additional File 3:
Performance of different profile similarity measures.
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Additional File 4:
Paralogs and orthologs among metabolic enzymes.
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Additional File 5:
Performance bias due to paralogous metabolic enzymes.
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Additional File 6:
Ortholog co-expression performance.
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Additional File 7:
Performance of protein fusion associations.
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Additional File 8:
Self-rank performance of phenotypic profiles.
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Additional File 9:
Effects of metabolite weighting and association-rank rescaling corrections.
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Additional File 10:
Alternating decision trees and related structures.
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Additional File 11:
Overlap in predictions based on different types of association evidence.
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Additional File 12:
Performance of predictions based on KEGG pathway membership.
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Additional File 13:
Sensitivity of prediction performance on the choice of excluded metabolites.
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Additional File 15:
Prediction performance with and without paralog exclusion.
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Additional File 16:
Gene coverage of different orthology datasets. Additional datasets, including pair-wise functional association matrices for different types of evidence and BLAST-based orthology datasets, are available on the authors' web site[63].
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Additional File 14:
Chromosome clustering using Gene Order vs. Gene Nucleotide Position.
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Additional File 17:
predictions.zip. Sample predictions of E. coli orphans. Additional datasets, including pair-wise functional association matrices for different types of evidence and BLAST-based orthology datasets, are available on the authors' web site[63].
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