Self-organizing maps (SOM) of TF expression in organ systems. (A) Portion of the TF expression matrix showing expression (colored boxes) in the appropriate stage ranges for each organ system and highlighting a section (54 of 152 TFs) of the foregut (FoGut) organ system cluster (blue). Rows are TFs and columns are organ systems, with a separate column for each stage range within an organ system (colors identical to Figure 2). The entire expression matrix is used as input to generate the SOM toroidal map. The toroid on the left displays the complete expression composite of all TFs expressed at stage range 13 to 16 and the toroid on the right highlights the FoGut TFs (blue) at the same stage range. The distribution of the FoGut TFs (blue filled circles) in two dimensions is shown in the lower panel. Co-expressed TFs (across all organ systems and all stages) will end up close to each other. (B) CNS TF map showing the dynamics of TF expression in a single organ system during development. The overall number of filled circles (=TFs) increases significantly at later stages, highlighting increased number of TFs and TF complexity. Two examples for TFs with different temporal dynamics are highlighted. (C) TF expression in the Hindgut, Foregut, and Endoderm/Midgut organ systems highlighting the relationships between the three organ systems. Intersecting filled circles (arrows show two examples) indicate expression in multiple systems; for example, at stages 4 to 6 only six TFs are co-expressed Hindgut and Foregut, while co-expression in midgut and hindgut/foregut is more common. (D) TFs in the PNS at stages 13 to 16 (center panel). The boxed region is expanded to the right. (E) Distinct and overlapping groups of TFs active in the PNS and SNS at stages 13 to 16 superimposed with the TFs active in the ectoderm/epidermis stages 4 to 6.
Hammonds et al. Genome Biology 2013 14:R140 doi:10.1186/gb-2013-14-12-r140