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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).
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BMC Genomics

ISSN: 1471-2164

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