Table I.

Boolean analysis of the responses of test sets of C- and light-responsive genes during the diurnal cycle and an extended night

A test set of 484 C-induced genes was generated by combining the 200 genes that are induced most strongly after adding 15 mm Suc for 3 h to C-depleted seedlings (Osuna et al., 2007); 200 genes that are induced most strongly after adding 100 mm Glc for 3 h to C-starved seedlings (Bläsing et al., 2005); and the 200 genes that are induced most strongly after illuminating 5-week-old plants for 4 h in 350 as compared to 50 ppm [CO2] (Bläsing et al., 2005; see gene lists). A similar approach was taken to generate a test set of 383 C-repressed genes. A set of 158 genes that respond rapidly to C was extracted from Osuna et al. (2007); these genes change by >log2 1.4-fold within 30 min of adding 15 mm Suc to C-starved seedlings. A test set of approximately 200 light-induced and 200 light-repressed genes was extracted from a treatment in AtGenExpress in which dark-grown seedlings were exposed to weak white light for 4 h (Bläsing et al., 2005; see gene list). Approximately 1,000 AKIN10-responsive genes were identified from Baena-Gonzalez et al. (2007). For each test set, genes were assigned values of −1, 0, or +1, depending upon whether they decreased, remained unaltered, or increased in a given time interval, using an arbitrary filter of 2-fold change. The time intervals were between the end of the day and end of the night, between the end of the night and 8 h into an extended night, and between 8 h and 24 or 48 h into an extended night. This gives in total 27 possible categories. Response classes that are qualitatively consistent with induction or repression by C are in bold and italic type, respectively. The table gives the numbers and the percent of the total C-repressed or C-induced genes in each class. Gene lists and assignments to the classes by the undirected and directed approach are provided in Supplemental Table S4. DC, Diurnal cycle; XN, extended night.

ClassDCXNXN LateC RepressedC InducedC Rapidly RepressedC Rapidly InducedLight RepressedLight InducedAKIN10 RepressedAKIN10 Induced
12−1003380922263
3−10−1110000080
9−1−10012012060
0−1−1−11430106141
100−10160223134
10−1−116100024675524
400−1617103486313
21−1−113554224512
111−1040200212
510−1702011107
811−110002000
6−11−110000001
701−100000000
13000332011019732730286
1410022012021326
2310130300001
1711090801009
26111800320190071
160101122020119
2501113283205003152
220012430422821355
24−1111362041116
15−11010000101
21−10115031113
18−1−1101000000
201−1100000000
190−1100000000