Advances in Bioinformatics / 2012 / Article / Tab 2

Research Article

Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

Table 2

The most prevalent (refined) event patterns in the EVEX data, considering only events with more than one gene or protein symbol, and their recursively nested events. These aggregated patterns refer to any type of regulation (*Reg), to binding events between two genes (Bind), and to any physical event (Phy) concerning a single gene such as protein-DNA binding, protein catabolism, transcription, localization, phosphorylation, and gene expression. The first two columns refer to the percentage of event occurrences covered by the given pattern and the cumulative percentage of event occurrences up to and including the pattern. The right-most column depicts the extracted gene pair and a coarse classification of its association type. and refer to gene symbols, and bindings are represented with ×. Further, means A regulates B, while expresses an indirect regulation.

Occ. Cum. occ. Event pattern Gene pair

58.6 58.6Phy(T:A)
15.0 73.6 *Reg(T:A)
8.4 82.0 *Reg(T:Phy(T:A))
8.0 90.0Bind(T:A, T:B)
4.7 94.7 *Reg(C:A, T:B)
3.8 98.5 *Reg(C:A, T:Phy(T:B))
0.2 98.7 *Reg(C:*Reg(T:Phy(T:A)), T:Phy(T:B))
0.2 98.9 *Reg(C:Phy(T:A), T:B)
0.2 99.1 *Reg(C:Phy(T:A), T:Phy(T:B))

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