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. 2008 May 12;102(1):127–140. doi: 10.1093/aob/mcn071

Table 2.

Comparison of gene expression levels of 14 selected differentially expressed genes estimated from quantitative real-time RT−PCR and microarray analysis

(A) Treatment × control
Accession number Functional annotation Quantitative RT−PCR fold change
Microarray fold change
HL vs. Control
CD848486 Putative ribosomal protein S12 (Oryza sativa) 1·3 1·84
CD848534 Lipid transfer protein (A. thaliana) 2·01 3
HL + HT vs. Control
CX947086 Beta-tubulin (Zinnia elegans) 1·49 2·04
CD847616 Aquaporin (Helianthus annuus) 2·69 2·48
CD847838 Oxidoreductase NAD-binding domain-containing protein (A. thaliana) 1·63 2·73
(B) Treatment × Organ
Quantitative RT–PCR fold change Microarray fold change
Accession number Functional annotation Leaves Immature seeds Leaves Immature seeds
HL × Organ
CD845834 Cysteine protease (Aster tripolium) 1·66 1 3·02 −1·83
CD845613 ss-1,3-glucanase (Cichorium intybus × Cichorium endivia) 2·91 −1·18 4·44 −1·62
CD849757 Expansin 3 (Zinnia elegans) −2·48 1·34 −1·33 2·08
HT × Organ
CD852690 Cytochrome P450 family protein (A. thaliana) −1·67 2·14 −1·90 1·78
CD850746 Pectin acetylesterase (EC 3·1·1.-) precursor − (Vigna radiata) 4·81 −1·4 2·57 −2·00
CD849228 Ferredoxin (Helianthus annuus) 2·85 1·17 5·17 −1·20
HL + HT × Organ
CD855563 Unknown protein (A. thaliana) −1·74 1·16 −1·41 2·32
CX943668 Esterase/lipase/thioesterase family protein (A. thaliana) 1·48 −2·27 3·01 −1·11
CD846383 Homeobox-leucine zipper protein (HD-ZIP protein 5) (A. thaliana) 1·4 1·74 3·61 1·01

Fourteen cDNA clones exhibiting different expression patterns and belonging to different functional categories were subjected to real-time RT−PCR analysis to confirm the microarray results. The expression levels of the target genes derived from RT−PCR were normalized using β-actin as an internal control and the fold-change values were calculated using the 2−ΔΔCT method and represent changes of mRNA abundance between the compared treatments. Fold-change values derived from the microarray analysis were computed as the difference between normalized expression values of the compared treatments. Positive values denote up-regulation and negative values denote down-regulation.