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The Search pages let users specify fields, or logical combinations of fields (14 fields are supported) to filter datasets.
DroID also contains gene expression and expression correlation data that can be searched and used to filter datasets, for example, to focus a study on sub-networks of co-expressed genes.
Instead of providing a simple binary cut-off approach, we provide a means to filter datasets in a biologically meaningful manner that catches the dynamic nature of many processes.
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The main characteristics of the filtered datasets are summarised in Table 1.
In both filtered datasets, the consecutive peaks and troughs associated with many of the passing bolts are easily discerned.
Hierarchical cluster analyses were performed using dChip software (www.dchip.org) on filtered datasets to identify temporal expression patterns of miRNA and mRNA levels in mouse lung development.
Filtered datasets of integration sites were analyzed for cross-contamination between samples processed on the same day and sequenced in the same Illumina run.
Applying both normalization methods to our filtered datasets we obtained similar results (data not shown).
Two filtered datasets were produced alongside an unfiltered dataset; these excluded reactions reported less than either twice or three times in the literature.
Using the filtered datasets as the myxozoan query set, this pipeline was implemented on RNA sequenced from encysted plasmodia of Myxobolus pendula (Fig. 1).
For hierarchical clustering, dissimilarity matrices were computed from filtered datasets using the 'diana' function ('cluster' package) and rendered as dendrograms using the 'dendro' function ('cluster' package).
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