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Figure 3 | BMC Bioinformatics

Figure 3

From: Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle

Figure 3

Refining clusters from Spellman et al.. (A) Refining the MCM cluster in [7]. The modules identified by MOFA differ not only in the set of TFs regulating the modules, but also in the different cell cycle phases to which they belong, providing a better understanding of how the cell regulates the complex expression program of the yeast cell cycle. Our results confirm previous findings that Mcm1 collaborates with Yox1 to regulate genes in M/G1 (e.g. YOR066W and CDC46) [30] and collaborates with Ndd1 and Fkh1/Fkh2 to regulate genes in G2/M (e.g. SPO12 and KIN3) [36]. (B) Refining the Y' cluster in [7]. The Y' cluster contains genes that share DNA sequence similarity and are found in Y' elements, which are located at chromosome ends. Spellman et al. [7] did not figure out how these genes are regulated. MOFA reassigns genes in the Y' cluster to three modules and identifies several possible regulators (Dat1, Gal4, Gat3, Hap1, Hap4, Msn4, Pdr1, Rap1 and Yap5), providing information for future experiments.

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