Metabolic Pathway Mapping of the Cytochrome P450 Superfamily via Co-Expression Analysis
This page is dedicated to the functional genomics of cytochrome P450 monooxygenases (CYP) in Arabidopsis thaliana. We aim to identify putative biochemical functions of so far uncharacterised members of this family. Therefore, public microarray data were analysed to identify known and putative metabolic genes co-expressed with each CYP across thousands of biological samples. Biochemical pathway annotation databases were curated for all co-expressed genes and used to place each P450s into putative biochemical pathways.
The Method in Brief
Expression data for 4,130 genes annotated in diverse databases and selected publications to be involved in a metabolic pathway were retrieved from the Genevestigator database covering ~1,800 biological samples. Upon background correction, we calculated the mean intensities from replicate arrays where applicable and divided the arrays in four groups: 1) Organ and tissue samples (compared to average intensity in all samples), 2) Stresss treated samples (compared to control samples) , 3) Hormone and otherwise treated samples (compared to control samples), and 4) Mutant derived samples (compared to equally treated wild type). We then used the expression data (log2-ratios) for each CYP to identify coexpressed genes using the ExpressionAngler algorithm using each of the four data sets. Each gene was manually curated regarding the annotation evidence (resulting in an annotation score for each gene). For each set of co-expressed genes we counted the scores and number of genes placed into any of the pathway annotations and thus identified co-expressed pathways. For more information refer to the Methods page
Structure of the Database
Below (and to the left) find a list of all CYPs present in Arabidopsis followed by a list of the top scoring co-expressed pathways, this links to the complete list of co-expressed pathways. In each PathwayMap find links to the four heatmaps detailing each co-expressed gene.
To find a gene by AGI locus (Atxgxxxxx) you may easiest use the Find (Ctrl-F) function of your browser.
You may also browse the list of pathways to find P450 genes co-expressed with genes in each pathway, this will also tell you which CYP is top scoring in a pathway of interest.
A Note on Browser Compatibility
These pages were created using OpenOffice Applications (Writer and Calc) and were tested with Mozilla Firefox and Microsoft InternetExplorer. These browser work fine, but you may need to adjust your text size (Tools/Text Size). Safari on Macintosh does display table boundaries in some pages even though they are supposed to be invisible, also a large white space appears at the top of some pages. Sorry Mac users, but I was not able to fix this...