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Table 1 Genome-wide statistics for different AuxRE variants.

From: Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome

AuxRE variant Total amount of genes with AuxRE (Z) Total amount of genes with conservative AuxRE Up-regulated
(1965 genes; 9.3%) 1
Down-regulated
(1916 genes; 9.1%) 1
    With AuxRE With conservative AuxRE With AuxRE With conservative AuxRE
    Amount (Xup) %, Xup/Z2 Amount (Yup) %, Yup/Xup3 Amount (Xdown) % , Xdown/Z2 Amount (Ydown) % , Ydown/Xdown3
TGTCTC 12635 4496 1221 9.7% 927 75.9% 1141 9.0% 746 65.4%
TGTCGG 5054 1696 449 8.88% 334 74.4% 454 8.98% 297 65.42%
TGTSTSBC 6829 1978 657 9.6% 504 76.7%* 605 8.9% 396 65.5%
AuxRE PWM 3799 1020 372 9.8% 290 78.0%* 354 9.3% 229 64.7%
AuxRE SGA 4679 1321 481 10.3%* 364 75.7% 438 9.4% 296 67.6%
AuxRE P&S 1779 468 191 10.7%* 158 82.7%** 167 9.4% 115 68.9%
  1. For the genes with predicted AuxRE in the [-1500; 5'UTR] region, the total amount and the amount of auxin-regulated genes are given. The AuxRE considered as conserved if its TGTC core could be found in an alignment of the regulatory region among A. thaliana, A. lyrata, T. halophile, C. papaya and C. clementine (See Materials and Methods). The set of auxin regulated genes created by meta-analysis of microarray data (Table 1) contains 1965 up- and 1916 down-regulated genes, which significantly (more than 1,5-fold, p < 0,05) changed their expression relative to control in more than three microarrays. The portion of auxin-regulated genes among the genes having an AuxRE variant was compared with an average portion of auxin responsive genes in the whole genome using the t-test for proportions (see Materials and Methods). The highest portions are shown in bold.
  2. 1Total number of auxin regulated genes and its portion from the whole-genome set (21098 microarray probes)
  3. 2The portion of auxin regulated among the genes having an AuxRE variant, compared with an average portion (1) by the t-test for proportions (*p < 0,05).
  4. 3Relation between conservation of an AuxRE variant in a gene promoter and its auxin responsiveness. To estimate the of statistical significance, the Y up /X up portion was compared by the t-test for proportions with 1442/1965 portion, as 1442 out of 1965 up-regulated genes contained any conserved position in a multiple alignment of the regulatory region. Y down /X down was compared with 1217/1916 portion (*p < 0,05; ** < 0,005).