Figure 5.

PAIR/GSLA reveals different mechanisms leading to similar phenotypes. A, The heme metabolism pathway plays an important role in the light development of Arabidopsis. This pathway produces essential components for both the light-synthesis machinery (especially the light-harvesting complex [LHC]) and the photoreceptor. The photoreceptor will change conformation after absorbing red/far-red light, which leads to ion fluxes and alterations in gene expression that initiate light development. B, In wild-type plants, protoporphyrin IX (Proto) is converted to Pchilde, then to Childe, and then used for the synthesis of chlorophyll or PΦB, which are essential components of the photoreceptor. In flu mutants (the green branch), defective FLU leads to the accumulation of Pchilde and, consequently, to a reactive oxygen species (ROS) burst. PCD is then triggered by the ROS burst. In fc mutants (the red branch), defective FC delays the conversion from Proto to PΦB and may deplete the supply of photoreceptor. An insufficient supply of photoreceptor may lead to the selective degeneration of defective chloroplasts. C, Functional categories and concept specificities of the terms reported by five gene-set annotation tools. GSLA reported all functional categories that were reported by other tools and the additional functional category of signal transduction, including GO:0008020 (G-protein-coupled photoreceptor activity). D, Functional categories and GO terms of the results of GSLA.