Predicting genes for orphan metabolic activities using phylogenetic profiles

doi:10.1186/gb-2006-7-2-r17

Genome Biology

Volume 7
Issue 2

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Predicting genes for orphan metabolic activities using phylogenetic profiles

Lifeng Chen and Dennis Vitkup

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

author email corresponding author email

Genome Biology 2006, 7:R17doi:10.1186/gb-2006-7-2-r17


Published:	15 February 2006

Subject areas: Bioinformatics, Biochemistry and structural biology

Additional 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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