The database then could be used to generate focused hypotheses that could be tested further experimentally and/or bioinformatically.
The resulting database or pool of the expression-pattern-linked nucleotides then could be used to generate focused hypotheses on the regulation of the tissue-specific expression of UGT1A isoforms.
Therefore, the identification of these expression pattern-linked nucleotides in different tissues provided potential working targets, both experimentally and/or bioinformatically, for testing and generating focused hypotheses on the mechanisms responsible for the tissue-specific expression of UGT1A isoforms.
Reported interactome data may also be utilized to conduct focused, hypothesis-driven research.
The emergence of high-throughput qPCR systems, e.g. the BioMark from Fluidigm, offers a platform that is ideal for the focused, hypothesis-driven study of gene expression of even small quantities of RNA [ 6, 7].
Although our focused, hypothesis-driven analyses justified this approach, it is possible that these results reflect a type I error arising from the number of comparisons conducted, rather than legitimate brain-behaviour relationships.
This more exploratory modus operandi (in contrast to a focused, hypothesis-driven approach) is likely to yield novel insights into form as well as function and, as shown in an exemplary fashion in case of our research on sea urchin morphology, will result in many new questions and hypotheses (Figs. 1, 2).
Moreover, application of multivariate exploratory techniques will generate clinically important and better focused hypotheses that would benefit encephalitis researchers in reducing the number of variables to be considered for further confirmatory statistical analysis.
Finally, despite whatever degree of immunopathogenesis or immunoprotection may have occurred in 1918, we see no particular reason to focus hypotheses on T-cell immunity over immunity conferred by antibody to viral antigens.
Our approach to querying multiple gene expression datasets using a seed network constructed from known interactions between specific genes of interest provides a promising strategy for focusing hypothesis-driven experiments using large-scale 'omics' data.
