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Table 2 Biological processes over-represented among (a) all the 966 L/C regulated genes in WT and 216 L/C misregulated genes in cli186, (b) the 542 L/C regulated genes in WT and the 92 L/C misregulated genes in cli186 that are connected in a network and (c) the 424 L/C regulated genes in WT and the 124 L/C misregulated genes in cli186 that are not connected in a network.

From: An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

   a ALL compared to genome b IN Network compared to multinetwork c NOT in network compared to genome
   WT cli186 WT cli186 WT cli186
Numerical Category MIPS Funcational Category L/C regulated (966) L/C misregulated (216) L/C regulated (542) L/C misregulated (92) L/C regulated (424) L/C misregulated (124)
01. METABOLISM 0.00163 - - - - -
01.01    amino acid metabolism - 0.0315 - - - -
01.02 nitrogen and sulfur metabolism - 0.01365 - - - -
01.02.01 nitrogen and sulfur utilization - - - - - -
01.05 C-compound/carbohydrate metabolism 0.04471 - - - - -
02. ENERGY 1.02E-07 2.01E-07 - - - 0.00042
02.01    glycolysis/gluconeogenesis 0.00175 0.00151 - - - -
02.13    respiration - 0.00119 - - - 4.71E-05
02.13.03 aerobic respiration - 0.02291 - - 0.00034 0.00264
02.30    photosynthesis 8.16E-05 2.53E-08 - 7.00E-03 0.00076 0.00316
10. CELLULAR COMMUNICATION/SIGNAL TRANSDUCTION - - - - - -
10.05    transmembrane signal transduction - - - - - -
10.05.02 non-enzymatic receptor mediated signaling 0.02932 - - - - -
10.05.02.30 ion channel mediated signaling pathway 0.02932 - - - - -
30. CONTROL OF CELLULAR ORGANIZATION - - - - - -
30.26    plastid - 8.63E-05 - - - 1.35E-05
30.26.03 chloroplast - 8.63E-05 - - - 1.35E-05
  1. This table shows the functional categories (funcats) annotated by MIPS [35] that respond to light and/or carbon among the 966 L/C regulated genes in wild-type (WT) and 216 L/C misregulated genes in cli186. The funcats are arranged according to their hierarchy as indicated by their numerical category. P-values to determine the significance of the funcats among the subsets of genes are shown in the columns labeled, 'L/C Regulated' and 'L/C Misregulated' in panels (a), (b) and (c). The p-values for the funcats that are significantly over-represented among both the L/C regulated genes in wild-type and the L/C misregulated genes in cli186 are in bold in panels (a), (b) and (c). The p-values for the funcats that are in normal text indicate those funcats that show over-representation among the 'L/C Regulated' or the 'L/C Misregulated' groups of genes in all panels, (a), (b) and (c). Dashes indicate no significant representation of the funcat among the groups of genes. Over-representation of MIPS terms in the gene lists were compared to the entire Arabidopsis genome (a), (c) or to the Arabidopsis multinetwork (b) using the BioMaps tool for visualization and statistical analysis, using a p value ≤ 0.05 [37, 38].