Method
Sequence-based prediction of protein-protein interactions by means of codon usage
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* Corresponding author: Reza Salavati reza.salavati@mcgill.ca
1 Institute of Parasitology, McGill University, Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec H9X 3V9, Canada
2 McGill Centre for Bioinformatics, McGill University, University Street, Montreal, Quebec H3A 2B4, Canada
3 Department of Biochemistry, McGill University, Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
Genome Biology 2008, 9:R87 doi:10.1186/gb-2008-9-5-r87
Published: 23 May 2008Additional files
Additional data file 1:
Distribution of d for each codon in yeast.
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Additional data file 2:
Comparison of the naïve Bayesian network and fully connected Bayesian network in the yeast gold standard positive set.
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Additional data file 3:
Comparison of the naïve Bayesian network and fully connected Bayesian network in the yeast gold standard negative set.
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Additional data file 4:
Variance over different components resulting from principal component analysis of the interacting gene pairs in yeast.
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Additional data file 5:
Comparison of PIC, PI-RSCU, PI-A and PI-L.
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Additional data file 6:
Comparison of PIP × PIC and the yeast gold standard positive set.
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Additional data file 7:
Per-complex comparison of PIP and PIP × PIC.
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Additional data file 8:
MIPS functional category enrichment for the yeast genome, PIP-Lcut600 and PIC-Lcut600.
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Additional data file 9:
Distribution of mRNA expression levels in interactions predicted by PIP-Lcut600 and PIC-Lcut600 for S. cerevisiae.
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Additional data file 10:
precision-recall curves for PIC, interolog mapping (INT), phylogenetic profiles (PGP), Rosetta stone (ROS), CAI coevolution (co-CAI) and CAI.
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Additional data file 11:
Precision-recall curves for PIC, PIT and PICT.
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Additional data file 14:
Results of performance of PIC on the P. falciparum gold standard set. For the performance of PIC on Escherichia coli gold standard set check reference [23].
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