An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in -1

R products (CYP-array) were retrieved from the 'Functional Genomics of Arabidopsis P450s' web page (Table 1). In this analysis, signal intensities in roots from 1 week old seedlings were generated by comparison to a 'universal RNA' sample [2]. Not detectable intensities were artificially set to a ratio of 0.05 compared to the 'universal control' and after log-transformation expression data were mean centered across the experiments. Expression data from published Affymetrix ATH1 array hybridizations were processed as described in Methods. The mean intensities from 17 experiments derived from young roots were selected. To generate a control similar to the 'universal RNA', mean intensities from 69 experiments covering similar samples were calculated and logratios were generated. Shown is a 2 × 2 plot comparing the mean centered expression ratios [log(sample/mean)] from both platforms using data for all P450 genes represented on both array types. Data points following the same trend are shown in black, points which are more than twofold different from the average expression in one platform, but less than twofold different in the other are shown in gray. Red dots indicate genes with opposing expression using the two platforms<p><b>Copyright information:</b></p><p>Taken from "An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in "</p><p>http://www.biomedcentral.com/1471-2229/8/47</p><p>BMC Plant Biology 2008;8():47-47.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2383897.</p><p></p

An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in -3

Ocessed as described in Material and Methods. Background corrected expression intensities were compared to untreated control experiments and log-ratios were used. Genes that are up- or down-regulated (>twofold) in more than 30% of each treatment group as indicated were selected. a) Number of P450s which are responsive to each treatment. b) Hierarchical cluster analysis with complete linkage. The resulting heatmap is color coded as indicated.<p><b>Copyright information:</b></p><p>Taken from "An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in "</p><p>http://www.biomedcentral.com/1471-2229/8/47</p><p>BMC Plant Biology 2008;8():47-47.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2383897.</p><p></p

An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in -4

S were retrieved from the Genevestigator database [10]. Background correction and ratio log-ratio generation was performed as describe in Methods. The expression vector of 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. Groups of samples are indicated on top of the heatmap. Mean-centered signal intensity ratios are color coded as indicated on the bottom of the heatmap. Genes with similarity to enzymes of the phenylpropanoid pathway are highlighted in orange. Genes related to lipid metabolism are highlighted in blue. Detailed information on the co-expressed genes and samples can be found in Additional File . To the right a section of the phenylpropanoid pathway is outlined in red and the putative duplicated pathway as hypothesized based on the co-expression analysis of CYP98A8 is outlined in orange.<p><b>Copyright information:</b></p><p>Taken from "An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in "</p><p>http://www.biomedcentral.com/1471-2229/8/47</p><p>BMC Plant Biology 2008;8():47-47.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2383897.</p><p></p

An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in -6

Ocessed as described in Methods. Expression vectors from the organ and tissue data sets of five genes (from was used as a bait for co-expression analysis comparing it's expression with that of all P450 genes. We retained five TTPS genes, which were co-expressed (r > 0.75) with at least one P450 in the organ and tissue expression data set, and the corresponding P450s (Table 2). This set of genes was used visualize expression. (in bold) and correlated genes with high correlation coefficients are color coded.<p><b>Copyright information:</b></p><p>Taken from "An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in "</p><p>http://www.biomedcentral.com/1471-2229/8/47</p><p>BMC Plant Biology 2008;8():47-47.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2383897.</p><p></p

Schematic representation of coumarin/furanocoumarin inheritance from the 4 ancestral taxa (pummelo, mandarin, citron, and papeda) in the cultivated <i>Citrus</i> species.

<p>Parental relations between species are illustrated by arrows. Thick arrows represent high chemotype similarities between hybrids and their ascendants. Same colors were used as in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142757#pone.0142757.g004" target="_blank">4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142757#pone.0142757.g005" target="_blank">5</a> for representing <i>Citrus</i> species. Coumarins and furanocoumarins are indicated in the same color as the ancestral taxon that transmitted them to their descendants. The symbol “+” indicates the probable transmission of compounds in the secondary species, while the symbol “-”indicates their disappearance.</p

List of the accessions investigated in the study and their phylogenetic constitution.

<p>List of the accessions investigated in the study and their phylogenetic constitution.</p

Coumarin and furanocoumarin quantities (mmol kg^-1 fresh weight) in the peel extracts of the 61 <i>Citrus</i> species investigated.

<p>Coumarins are represented in orange; furanocoumarins of the bergapten cluster, in blue; furanocoumarins of the xanthotoxin cluster, in red; and furanocoumarins of the isopimpinellin cluster, in green. Ancestral taxa and secondary species are highlighted in the bottom of the graph. Sweet mandarins are presented in bright red, and acidic mandarins are illustrated in deep red.</p

Heatmap displaying the coumarin and furanocoumarin profiles in the pulp of the 61 <i>Citrus</i> species investigated.

<p>A: heatmap; B: dendrogram of compounds; C: dendrogram of <i>Citrus</i> varieties. A red square highlights the presence of a given compound, while a yellow square shows its absence. Coumarins are represented in orange; furanocoumarins of the bergapten cluster, in blue; furanocoumarins of the xanthotoxin cluster, in red; and furanocoumarins of the isopimpinellin cluster, in green.</p

NJ analysis of the 23 citrus varieties belonging to the 4 ancestral taxa based on the coumarins and furanocoumarins contents in peel expressed as mg.kg^-1 fresh weight.

<p>Numbers in black represent the bootstrap probability values. The colors correspond to the phylogenetic constitution of the varieties and are indicated in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142757#pone.0142757.g002" target="_blank">2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142757#pone.0142757.g003" target="_blank">3</a>.</p

Heatmap displaying the coumarin and furanocoumarin profiles in the peel of the 61 <i>Citrus</i> species investigated.

<p>A: heatmap; B: dendrogram of compounds; C: dendrogram of <i>Citrus</i> varieties. A red square highlights the presence of a given compound, while a yellow square shows its absence. Coumarins are represented in orange; furanocoumarins of the bergapten cluster, in blue; furanocoumarins of the xanthotoxin cluster, in red; and furanocoumarins of the isopimpinellin cluster, in green.</p