Figure 3

Worm-fly modules resulted from OrthoClust. (A) The co-appearance matrix of worm and fly genes. The worm and fly genes were sorted separately. Blocks along the diagonal are modules of worm and fly. Some blocks along the diagonal have strong co-appearance at the off-diagonal positions (see red circles as an example). These are conserved modules across worm and fly. In such modules, the corresponding worm and fly genes show strong overlap of Gene Ontology (GO) terms (P = 3.3 × 10^-16, hypergeometric test). There are blocks along the diagonal that have no overlap at the off-diagonal positions (the blue pentagon and the green hexagon). They are the worm-specific and fly-specific modules. Such modules have rare overlap in terms of their GO terms (P = 0.035, hypergeometric test). (B) Enriched GO terms of a conserved module in worm and fly. Each circle represents a GO term, and the color code stands for statistical significance. The terms project onto a semantic space in which the geometric distance between GO terms mirrors their sematic distance. GO terms with similar meanings are packed together. GO terms correspond to fundamental functions like RNA biology, cell cycle, and so on.