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To overcome this limitation, we developed a new module discovery method termed BEEM (Biclusering-based Extraction of Expression Modules) in order to discover expression modules that are functional in a subset of tissues.
With that in mind, the two strains were first compared entirely separately from each other to discover expression differences in response to pathogen exposure for each strain.
The results presented here suggest that this analysis can help to discover expression signatures of miRNAs and their target mRNAs that can be employed for therapeutics in human cancers.
Second, the initial gene subset selection based on the Genbank search may have diminished the opportunity to discover expression differences among genes not otherwise known to be related to sepsis.
One strategy for the discovery of cis and trans acting genes is to use gene expression as a phenotype and to map associations between thousands of markers and the expression of thousands of genes in hundreds of samples to discover expression quantative trait loci (eQTL) [ 2, 3].
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This result demonstrates that, from the multiple tissue transcriptomes, BEEM successfully discovered expression modules that cannot be captured by the traditional approaches.
Newly in this study discovered expression domains are shown in bold.
Previously, we discovered expression of AP-2 ε in murine hypertrophic chondrocytes and in human articular cartilage.
The unexpected induction of defensin 3 and thaumatin in response to starvation is in agreement with the recently discovered expression of antimicrobial peptides in food-deprived Drosophila melanogaster.
The role of dysregulated genes in cancer is generally difficult to determine [ 72], but the discovered expression profiles among ERGs were remarkable.
This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept.
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