Journal: BMC Genomics
Article Title: Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o , p' -DDT
doi: 10.1186/1471-2164-9-487
Figure Lengend Snippet: Comparative analysis of global gene expression profiles elicited by o , p '-DDT . (A). Comparative gene expression analysis between EE-treated mouse, o , p' -DDT-treated rat and o , p' -DDT-treated mouse. A total of 996 orthologs were represented on the rat cDNA microarray, mouse cDNA microarray and mouse Agilent oligonucleotide microarrays determined by HomoloGene . 538 of these orthologs showed a |fold change| ≥ 1.5 for at least one time point in either species. These 538 differentially expressed orthologs were subjected to hierarchical clustering. The dendrogram illustrates that mouse o , p' -DDT gene expression profiles are more similar to rat o , p' -DDT gene expression profiles than the mouse EE gene expression profiles. (B) Correlation analysis using differentially expressed orthologous genes. The temporal profiles of o , p' -DDT-treated mouse liver (current study) and those of the o , p' -DDT-treated rat liver were compared by determining the Pearson's correlation of the temporal gene expression (fold change) and significance (p1 [ t ] value) between orthologs. Both studies used comparable study designs and data analysis methods, although different platforms were used (i.e., rat cDNA microarray and mouse Agilent oligonucleotide microarray). 140 genes were identified as differentially expressed orthologs. (C) Scatter plot of the 140 differentially expressed orthologous genes. Correlations for gene expression and significance approaching 1.0 indicate that the behavior or the orthologous genes are similar and would fall in the upper right quadrant. Orthologs tended to localize in upper- or lower-right quadrant (32.9% and 47.9% of total number of spots, respectively), indicating that temporal gene expression changes for o , p' -DDT-treated mouse and rat liver are comparable. However, poor correlations between the temporal p1( t ) values and gene expression fold changes would fall within the lower left quadrant. For example, Cyp17a1 fell into this quadrant suggesting that significant differences exist between the rat and mouse ortholog expression profiles.
Article Snippet: Whole Mouse Genome 4 × 44 K Oligo Microarray Kit (Agilent Technologies, Inc, Santa Clara, CA) was used for global gene expression analysis.
Techniques: Expressing, Microarray
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![<t>Microarray</t> and QRT-PCR results . (A) Identification of differentially regulated genes. (B) Number of differentially expressed genes following o , p' -DDT treatment in the mouse liver. Differentially expressed genes were selected based on a p1( t ) ≥ 0.999 at two or more time points and an absolute fold change ≥ 1.5 at one or more time points relative to time-matched vehicle controls. All differentially expressed genes are listed in Additional file . (C) Verification of microarray results by QRT-PCR. QRT-PCR results relative to time-matched vehicle controls are shown as bar and presented as mean ± SE. Microarray results are represented as lines. The dashed line indicates the expression level of the time-matched vehicle control. The asterisk (*) indicates a significant ( p < 0.05) difference from the time-matched vehicle controls for QRT-PCR, n = 5. (D) Hepatic expression of PXR/CAR-target genes in o , p' -DDT-treated mouse. A heat map of o , p' -DDT elicited microarray expression profiles for selected PXR-, CAR-specific and PXR/CAR-shared target genes identified in the literature [ - ]. While some CAR-regulated genes such as Cyp1a1 , Fmo5 , Sult1d1 or Abcc2 were moderately induced, several PXR-target genes, including ApoA4 , Ces2 , Gstm2 or Insig2 , exhibited strong induction. However, other PXR-target genes such as Hmgcs1 and Hmgcs2 were down-regulated.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_7663/pmc02577663/pmc02577663__1471-2164-9-487-2.jpg)
![Comparative analysis of global gene expression profiles elicited by o , p '-DDT . (A). Comparative gene expression analysis between EE-treated mouse, o , p' -DDT-treated rat and o , p' -DDT-treated mouse. A total of 996 orthologs were represented on the rat cDNA microarray, mouse cDNA microarray and mouse Agilent oligonucleotide microarrays determined by HomoloGene . 538 of these orthologs showed a |fold change| ≥ 1.5 for at least one time point in either species. These 538 differentially expressed orthologs were subjected to hierarchical clustering. The dendrogram illustrates that mouse o , p' -DDT gene expression profiles are more similar to rat o , p' -DDT gene expression profiles than the mouse EE gene expression profiles. (B) Correlation analysis using differentially expressed orthologous genes. The temporal profiles of o , p' -DDT-treated mouse liver (current study) and those of the o , p' -DDT-treated rat liver were compared by determining the Pearson's correlation of the temporal gene expression (fold change) and significance (p1 [ t ] value) between orthologs. Both studies used comparable study designs and data analysis methods, although different platforms were used (i.e., rat cDNA microarray and mouse Agilent oligonucleotide microarray). 140 genes were identified as differentially expressed orthologs. (C) Scatter plot of the 140 differentially expressed orthologous genes. Correlations for gene expression and significance approaching 1.0 indicate that the behavior or the orthologous genes are similar and would fall in the upper right quadrant. Orthologs tended to localize in upper- or lower-right quadrant (32.9% and 47.9% of total number of spots, respectively), indicating that temporal gene expression changes for o , p' -DDT-treated mouse and rat liver are comparable. However, poor correlations between the temporal p1( t ) values and gene expression fold changes would fall within the lower left quadrant. For example, Cyp17a1 fell into this quadrant suggesting that significant differences exist between the rat and mouse ortholog expression profiles.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_7663/pmc02577663/pmc02577663__1471-2164-9-487-3.jpg)
