Method
Predicting genes for orphan metabolic activities using phylogenetic profiles
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* Corresponding author: Dennis Vitkup vitkup@dbmi.columbia.edu
Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, St Nicholas Avenue, Irving Cancer Research Center, New York, NY 10032, USA
Genome Biology 2006, 7:R17 doi:10.1186/gb-2006-7-2-r17
Published: 15 February 2006Additional files
Additional File 1:
Genomes used in this study to generate phylogenetic profiles.
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Additional File 2:
The effect of connection specificity adjustment.
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Additional File 3:
Comparison of the performance of the simplex and simulated annealing algorithms.
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Additional File 4:
Comparison of the predictions based on Equations 2 and 3.
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Additional File 5:
Ten-fold cross-validation of the algorithm.
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Additional File 6:
Comparison of the predictions based on all yeast non-metabolic genes as the candidate gene set, all hypothetical genes or a randomly selected subset of yeast non-metabolic genes.
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Additional File 7:
Context-based association as a function of metabolic network distance in E. coli.
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Additional File 8:
Comparison of predictions based on normalized gene phylogenetic profiles, mutual information, and the method reported in the paper.
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Additional File 9:
Dataset of sample predictions for E. coli and S. cerevisiae orphan activities.
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