Fig. 2: Construction of TO-GCNs and the enriched pathway in the primary feather transition.
From: Conserved regulatory switches for the transition from natal down to juvenile feather in birds
The TO-GCNs of TF genes were constructed from normalized gene expression levels during embryonic (a) and juvenile feather (b) developments. In a TO-GCN, each blue node represents a TF gene and each grey line represents a co-expression relationship between two TF genes. The number in each level represents the number of TF genes at that level. The mean z-score of TF gene expression at each level was used to generate the bar charts and heatmap. The raw input is shown in the Source Data file. c The proportion of TF genes in TO-GCN level differences. Most TF genes show less than 3-level differences between embryonic and juvenile feathers. Embryonic (juvenile) specific TFs indicate TFs that are specifically upregulated in levels bigger than 8 in natal downs (juvenile) but not in juvenile (natal downs) feathers. All the specific TFs for natal downs and juvenile feathers are labeled. ID3 is the control. d SISH of BNC1 shows distinct patterns between the two feather types (barb tips of embryonic feather and whole barbs of juvenile feather) while ID3 is expressed similarly between the two feather types (n = 3 biologically independent chicken skins). e The pathways enriched in more than one level were selected from Supplementary Data 4. Epi epidermis; Der dermis; FF feather filament; Skin whole skin; L level of TO-GCN; GO gene ontology; FDR false discovery rate. Scale bar: 100 µm.
