Prediction of evolutionarily conserved interologs in Mus musculus

Additional file 1:

A list of interactions transferred from other organisms to Mus musculus and interactions identified experimentally in Mus musculus. Columns A and B show a pair of Entrez Gene IDs of interacting proteins in Mus musculus; Columns C and D show the corresponding GIs of interacting proteins in Mus musculus; Columns E and F show the corresponding GIs of interacting proteins in reference organism; Column G shows an experimental method used to identify the interaction in reference organism; Column H shows PubMed IDs of the article in which the interactions were reported; Column I shows the name of the reference organism in which the interaction was identified; and Column J shows the source of the interaction of reference organism.

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Additional file 2:

A list of genomes used for phylogenetic profile analysis and operon prediction. For the phylogenetic profile analysis 26 genomes of eukaryote species and 186 genomes of bacterial species were used. The 186 genomes of bacterial species were also used for operon prediction.

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Additional file 3:

A list of interactions in Mus musculus, which were transferred from operons of bacterial species. Columns A and B show a pair of the Entrez Gene IDs of interacting proteins in Mus musculus; Columns C and D show the corresponding GIs of interacting proteins in Mus musculus; and Column E shows the co-occurrence frequency of Mus musculus protein orthologs in bacterial operons.

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Additional file 4:

ROC Graph for prediction of protein – protein interactions. The ROC curve is a plot of "sensitivity (True positive rate)" versus "1 – specificity (False positive rate)." The "sensitivity" and "1 – specificity" values at the point near the upper left corner are 0.82 and 0.13, respectively, where the balanced accuracy for prediction of protein – protein interaction reaches the maximum (86%).

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Additional file 5:

Accuracy of cross validation in phylogenetic profiles. A table shows the number of true positives (TP), false negatives (FN), true negatives (TN), and false positives (FP) in each step of five-fold cross validation trials. Sensitivity and Specificity are calculated according to the formula described in the Methods section. The accuracy reaches the maximum in the 4^th step of cross validation trials.

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Additional file 6:

A list of filtered interactions in Mus musculus, which were transferred from operons of bacterial species and filtered with the phylogenetic profiles method. Columns A and B show a pair of the Entrez Gene IDs of interacting proteins in Mus musculus; Columns C and D show the corresponding GIs of interacting proteins in Mus musculus; Column E shows the co-occurrence frequency of Mus musculus protein orthologs in bacterial operons; and Column F shows the Pearson correlation co-efficient between the phylogenetic profiles of mouse proteins.

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Additional file 7:

Interologs and experimentally identified interactions in Mus musculus obtained after filtering with the phylogenetic profiles method. Columns A and B show a pair of the Entrez Gene IDs of interacting proteins in Mus musculus; Columns C and D show the corresponding GIs of interacting proteins in Mus musculus; Columns E and F show the corresponding GIs of interacting proteins in reference organism; Column G shows the experimental method used to identify the interaction in reference organism; Column H shows the PubMed IDs of the article, in which the interactions were reported; Column I shows the name of the reference organism, in which the interaction was identified; Column J shows the source of the interaction of reference organism; and Column K shows the Pearson correlation co-efficient between the phylogenetic profiles of mouse proteins.

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