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eFP-tissue expression

​​​​​The eFP browser provides an intuitive pictographic view of expression data across a diverge range of cDNA microarray datasets. It is implemented using the source code for the arabidopsis eFP (electronic Flourescent Pictogrpah) browser, hosted at the Bio-Array Resource. The datasets currently implemented largely reflect our own research interests and those of UPSC more widely as well as reflecting the bias of currently available array data in poplar. We will expand the number of views as we collate additional array datasets. 

 

Currently, four pictographic views are implemented.  These cover the processes of leaf (four experiments) and wood (six experiments) development in both field and greenhouse conditions, biotic and abiotic stress response (14 experiments) and the comparison of expression between different tissues types (two experiments).  The majority of this data is hosted at UPSC-BASE.

 

A key difference between the data represented in our eFP browser implementation and the original eFP browser is that all of the data we currently present is collected from cDNA arrays and is therefore all ratio-based. The poplar data is also collected from a divergent range of species and genotypes, whereas the majority of the arabidopsis data is collected from a single ecotype.

 

As well as viewing array data in pictorial view, users can also download the expression values used to generate each pictograph for secondary uses. For publication, data can be plotted using the exPlot tool, which produces figures more suitable for publication.  

 

Although perhaps obvious, it is worth remembering that information can only be displayed for a gene if that gene is represented on the array used. The most extensive array used to generate the data in exImage represents ~1/3 of the poplar genome. As this means the majority of genes will not contain any data, we have provided a tool to filter a list of gene model or EST IDs and indicate which ones are represented on which array platform.

 

For all experiments other than the stress datasets, all expression ratios represent comparrison to a common reference pool, for example created by pooling material across all tissues or sample dates. In the case of the stress data, all ratios represent treatment/control. Detailed information can be found in the relevant publications for each dataset. 

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