Table 1
32 Gene regulatory modules with high correlation coefficients and other supports
Correlation coefficient Most enriched biological process* TF Gene Coherence† I$ M& L#
0.989913 lipid transport 7 62 6 Ce √ √ [27]
0.945372 positive regulation of release of sequestered calcium ion into cytosol 7 11 36 √ [36]
0.930583 vegetative to reproductive phase transition of meristem 8 161 3 Ce √ √ [37,38]
0.926575 proteolysis 8 27 18 E √ √ [39]
0.910277 steroid biosynthetic process 7 81 3 √ √ [40]
0.902439 photosynthesis 9 114 12 T √ [41]
0.898638 protein transport 9 183 8 Ce √
0.896121 regulation of cell shape 8 50 6 E&H
0.893346 ATP-dependent chromatin remodeling 6 163 1 E √
0.890829 photosynthesis, light harvesting 11 102 12 √ √ [41]
0.888479 mRNA processing 9 218 7 Ce √
0.882899 translational elongation 9 85 4 E √
0.880672 regulation of flower development 9 57 7 Ce √ √ [42]
0.867582 lipid transport 7 63 6 Ce √
0.862264 skeletal system morphogenesis 9 70 4 T √
0.857502 translation 11 125 12 Ce
0.855305 carotenoid biosynthetic process 9 103 3 Ce √
0.852366 lactate metabolic process 7 84 4 E,T&H √
0.843827 establishment or maintenance of polarity of embryonic epithelium 5 99 6 E √
0.841523 flavonoid biosynthetic process 8 44 6 E √ √ [29]
0.836985 base-excision repair 10 36 8 E
0.830088 flavonoid biosynthetic process 9 38 15 E&T √ √ [29]
0.826087 acetyl-CoA biosynthetic process 7 158 3 E √ [43]
0.824363 auxin mediated signaling pathway 12 76 5 E √ √ [44]
0.820377 carbohydrate metabolic process 9 71 11 T √ [45]
0.817311 transcription 9 56 25 E √
0.81347 superoxide metabolic process 10 46 6 T
0.812358 nodulation 10 73 4 E √ √ [28]
0.809849 PSII associated light-harvesting complex II catabolic process 8 108 2 E&Ce √ √ [45]
0.808305 metabolic process 7 44 13 T √
0.806202 secondary cell wall biogenesis 8 97 6 E √ √ [46]
0.804089 DNA replication initiation 10 96 4 Ce √

Column 1 lists the average of the pairwise Pearson’s correlation coefficients of expression values of genes in these modules. Column 2* reports the most significantly enriched GO biological process in each module that has the smallest p-value. Column 3 lists the number of TFs predicted for a module. Column 4 lists the number of genes in a module that had GO annotations. Column 5† lists the percent of genes in each module participating in the biological process. Column 6 (I$) shows if at least two predicted TFs in a module interacted according to the STRING predictions and the BLAST homology search. Evidence sources for STRING predictions include E - experiments; Ce - co-expression; T – text mining; H - homology. Column 7 (M&) reports if the DNA binding motifs of some predicted TF families in a module matched the motifs extracted from the upstream sequences of the regulated genes in the module. Column 8 (L#) lists if previous literature had reported a relationship amongst at least one predicted TF family, a stress condition, and the predicted gene function of a module.

Zhu et al. BMC Genomics 2012 13:437   doi:10.1186/1471-2164-13-437

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