Nine branch thresholds were used.
Coexpression modules are defined at multiple branch thresholds.
Differentially expressed genes comprising signature 1. Genes within signature 1 and sub-signatures defined at more stringent branch thresholds are ranked based on overexpression in localised prostate cancer within dataset GSE3325.
A reduction of the branching threshold in the basal metamers was required to generate a realistic WT branching pattern (F ).
Without local basal reduction of the branching threshold (T, black arrow), the most basal metamer always produced a branch (E ).
We adjusted the model by locally reducing the branching threshold in the most basal metamers of the gametophore (assumption 4; Figure 2 figure supplement 2).
Unless this process was considered in the context of a larger species tree, it is unlikely that the GMYC would identify a significant branching threshold.
Additional file 4: Table S2 provides a complete list of coexpressed genes signatures generated used the Ward approach at all branching thresholds.
In addition gene signatures are defined as sub-signatures of larger signatures generated using lower stringencies/broader branching thresholds, the relationship between gene signatures at different thresholds is indicated in columns X-AE.
