Figure 1.

Preparation of the training data set for the inference of functional associations between Arabidopsis genes. High-confidence physical protein-protein interactions were collected from four databases as positive examples. Evidence for six types of functional associations was collected from 12 public databases. Thirty features were computed from these data and evaluated for their ability to discriminate protein interactions from random gene pairs. Sixteen high-quality features with area under the curve (AUC) > 0.6 were used to represent each gene pair. Random gene pairs other than positive examples were used as negative examples. The number of negative examples was 100 times the number of positive examples.