Fig. 1.

Tree-based organization, redundancy reduction, and partitioning of data. (A) All available data from in vivo and in vitro experiments for kinase, SH2, and PTB domains are organized by mapping them onto the phylogenetic domain trees. (B) The tree data structure enables us to automatically compile a data set of positive and negative examples for each domain or family of related domains. For a given domain (leafs in the tree) or domain family (branch points in the tree), we exclude phosphorylation sites that cannot be unambiguously designated as positive or negative examples, because they were annotated at a higher level in the tree. (C) Redundant phosphoproteins and phosphorylation sites are identified and eliminated on the basis of sequence similarity of the full-length protein sequence or the phosphorylation sites themselves. (D) Each redundancy-reduced data set is partitioned into four parts that are used for training, test, and validation of ANNs. See fig. S1 for a flowchart of the pipeline, fig. S2 for an overview of the data coverage, and Methods for details.