Fig. 1. A summary of the seedling phenotypes of the photomorphogenic mutants and their genome expression profile relatedness. (A) Morphological comparison of dark-grown Arabidopsis wild-type (WT), pleiotropic cop/det/fus and partial photomorphogenic mutant seedlings. All seedlings were 6-day-old. Scale bars: (in cop1-1 panel for top row) 1 mm. (B) Morphological comparison of continuous white light-grown wild-type (WT) and pleiotropic cop/det/fus mutant seedlings. All seedlings were 6-day-old and photographed at the same magnification. Some of the mutants shown in A and B were used in studies reported in C and D, while some were used in studies reported in subsequent Figures. (C) Hierarchical clustering analysis of overall relatedness for expression ratios from wild-type seedlings grown under normal white light (WL) versus dark-grown (D) siblings, and dark-grown pleiotropic cop/det/fus and partial photomorphogenic mutants versus dark-grown wild-type seedlings of the same ecotype. An expression profile from dark-grown tir1-1 versus dark-grown wild-type seedlings is also included for comparison. Only those genes that exhibited twofold or more differential expression in at least one sample pair of the 13 tested were included. There are 3057 genes included in the cluster analysis (see supplementary data at http://dev.biologists.org/supplemental/ or http://plantgenomics.biology.yale.edu/ for more information). Asterisks denote the ecotype of wild-type Arabidopsis: ^*for Col-0 and ^**for WS. (D). Hierarchical clustering analysis of overall relatedness for expression ratios from wild-type seedlings grown under normal white light (WL) versus dark-grown siblings, and high intensity light-grown (HWL) pleiotropic cop/det/fus mutants versus normal white light-grown wild-type seedlings of the same ecotype. Only those genes that exhibited twofold or more differential expression at least in one sample pair of the nine tested were included for comparison. There are 2608 genes included in the cluster (see supplementary data at http://dev.biologists.org/supplemental/ or http://plantgenomics.biology.yale.edu/ for more information). Asterisks denote the ecotype of wild-type Arabidopsis as in A.