Figure 3

Overlap matrices of regulatory modules. (a) Overlap matrices between EPMs in all the three conditions. The OLs were calculated as the proportion of the intersection genes in the smaller EPM (minOL). The enriched GO categories of each EPM are also shown as several colored dots. Black-lined boxes represent the EPMs that are significantly overlapped across all the three conditions. 'A' indicates the overlapped stress-related EPMs represented by the three boxes linked by dashed lines. They have the common regulators Msn2/4 and Hsf1. Identically, the EPMs indicated as 'B' have the common regulators Rap1, Sfp1 and Fhl1. The EPMs indicated as 'C' have Mbp1, Swi4, Swi6 and Stb1 as their common regulators. Black arrows indicate EPMs that are highly overlapped between the heat shock and nitrogen depletion conditions. (b) Overlap matrices between RMs (minOL). Several RMs, which were included in the distinct EPMs in the nitrogen depletion and cell cycle conditions, are significantly overlapped with the RMs in heat shock EPM 11.