An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

Additional File 1:

Locus and probe set information for P450s. Given are the Affymetrix AtH1 microarray probe sets used for cytochromes P450 and the name and AGI loci recognized by these probe sets. In addition, the number of experiments in the respective data sets with detectable expression (more than twofold difference from the control) is given, as well as the fraction of samples with detectable expression. In the organ data sets control is defined for each probe set as the average signal intensity on arrays were this probe set was called 'absent' by the Affymetrix software. In the stress and hormone data sets control is defined as the signal intensities of untreated control samples. In the mutant data set control is defined as the signal intensities in the corresponding wild type samples.

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Additional File 2:

Stress responsive expression of P450s. Microarray expression data were retrieved from the 'Genevestigator' database and processed as described in Methods. Only genes that are up-regulated (>twofold) in more than 30% of at least one treatment group as indicated on top were selected. Background corrected expression intensities were compared to untreated control experiments and log₂-ratios were used for hierarchical cluster analysis with complete linkage. The resulting heatmap is color coded as indicated in the overview image in Sheet 1 (overview). Details on the individual samples can be found in Sheet2 (details) of this spreadsheet.

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Additional File 3:

Pathway predictions based on co-expression analysis of P450s with known functions. Top scoring co-expressed pathways for P450s with characterized biochemical functions.

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Additional File 4:

Co-expression analysis using CYP73A5 encoding cinnamate 4-hydroxylase as bait. Data from published Affymetrix microarrays (representing a) 167 organ and tissue samples and b) 243 stress related treatments) were retrieved from the Genevestigator database [10]. Background correction and ratio log2-ratio generation was performed as describe in Methods. The expression vectors of CYP73A5 were compared to those of 4,119 genes annotated in diverse databases to be involved in any metabolic pathway using the 'ExpresionAngler' algorith [9]. Expression profiles of co-expressed genes with a correlation coefficient of more than 0.5 are shown as a heatmap. Groups of samples are indicated on top of the heatmap. Mean centred signal intensity ratios are colour coded as indicated on the bottom of each heatmap. Genes encoding enzymes of the phenylpropanoid and shikimate pathways are highlighted in red and green, respectively. Sheet 1 shows overview image, detailed information on the co-expressed genes and samples can be found in sheets 2 (organs) and 3 (stress) of this file.

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Additional File 5:

Co-expression analysis using CYP98A8 as bait. Data from published Affymetrix microarrays representing 167 organ and tissue samples were retrieved from the 'Genevestigator' database [10]. Background correction and ratio log₂-ratio generation was performed as describe in Methods. The expression vector of CYP98A8 was compared to those of 4,119 genes annotated in diverse databases to be involved in any metabolic pathway using the 'ExpresionAngler' algorithm [9]. Expression profiles of co-expressed genes with a correlation coefficient of more than 0.6 are shown as a heatmap table. Brief descriptions of the experiments and the experiment identifier from the 'Genevestigator' database are indicated on top of the heatmap. Mean-centred signal intensity ratios are colour coded as indicated to the right.

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Additional File 6:

Co-expression analysis using CYP98A8 as bait. Data from published Affymetrix microarrays representing 167 organ and tissue samples were retrieved from the Genevestigator database [10]. Background correction and ratio log2-ratio generation was performed as describe in Methods. The expression vector of CYP97A3 was compared to those of 4,119 genes annotated in diverse databases to be involved in any metabolic pathway using the 'ExpresionAngler' algorithm [9]. Expression profiles of co-expressed genes with a correlation coefficient of more than 0.84 are shown as a heatmap table. Brief descriptions of the experiments and the experiment identifier from the Genevestigator database are indicated on top of the heatmap. Mean-centered signal intensity ratios are color coded as indicated to the right. This table corresponds to Figure 6.

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Additional File 7:

Cluster analysis of triterpene synthases (TTPS) and P450s. Microarray expression data were retrieved from the 'Genevestigator' database and processed as described in Methods. Expression vectors from the four data sets of all twelve TTPS genes from A. thaliana were used as bait for co-expression analysis comparing its expression with that of all P450 genes. We retained seven TTPS genes, which were co-expressed (r > 0.75) with at least one P450 in at least one of the four expression data sets and the corresponding P450s (Table 2). This set of genes was used for hierarchical clustering with complete linkage in a) the organ expression data set and b) the mutant data set as shown in the overview image in Sheet 1. TTPS and clusters with P450 genes with high correlation coefficients are colour coded. Detailed information on the co-expressed genes and samples can be found in sheets 2 (organs), 3 (stress), 4 (hormones), and 5 (mutants) of this file. The numbers in brackets refer to the experiment ID from the Genevestigator database.

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