Figure 4

Gene ontology of HVC transcriptomes (A-D) and RA transcriptomes (E) related to season (A,C,E), to testosterone (B), and to the area-specific presence/absence of androgen and estrogen receptors (D) (see Materials and methods sections M10 , M11 and M15 for details). Biological processes typical of neuronal differentiation and synaptic transmission are depicted in colour; all others are depicted in grayscale. Due to space limitations, we could not include the names of all significant biological processes in the charts, but we list them in Additional file 5. (A) Of the seasonal biological processes of up-regulated genes of LD HVC versus SD HVC, 34.9% (sum of the coloured segments) relate to synaptic transmission and neuronal differentiation, which includes neurogenesis. (B) Testosterone-induced biological processes of up-regulated genes of HVC of SD + T males versus SD HVC; 36.8% of the biological processes are related to synaptic transmission and neuronal differentiation. (C) None of the seasonal biological processes of down-regulated genes of LD HVC versus SD HVC concern typical neuronal categories. (D) Area-specific biological processes of up-regulated genes of LD HVC versus LD ENT; 30.6% of these HVC-specific processes relate to synaptic transmission and neuronal differentiation. (E) Seasonal biological processes of up-regulated genes of LD RA versus SD RA concern general cell biological processes but not neuronal differentiation. (F) Differentially expressed HVC transcriptomes (genes that are significantly up- or down-regulated in HVC versus ENT) depend on elevated levels of testosterone. The ‘LD male’ curve shows the good agreement between the two techniques for assessing the differential expression of HVC genes (R² = 0.85) of different groups of LD males, whereas the transcriptomes do not correlate well between LD and SD males (‘SD male’ curve with R² = 0.46) but do so between LD and SD + T males (‘SD + T male’ curve with R² = 0.79).