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That is, we consider the interaction between two expression phenotypes under categorical genotypes which thus have not been examined in GWA.
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The rationale behind differential co-expression analysis is that changes in gene co-expression patterns between two contrasting phenotypes (e.g., healthy and disease) provide hints regarding the disrupted regulatory relationships or affected regulatory subnetworks specific to the phenotype of interest (in this case, the disease phenotype).
Importantly, some gene itself may not show differential expression between two phenotypes, but may play an important role in interconnecting other differentially expressed genes in PPI network [ 14].
A method called Clipper exploits network topology to detect signaling paths within longer pathways based on differential gene expression between two phenotypes [ 20].
To do so, it offers well-established statistical methods in addition to a new method to calculate differential pathway expression between two user-supplied phenotypes.
In adult zebrafish, Johnston et al. (2009) demonstrated significant differences in miRNA expression between two fast muscle phenotypes, myotube recruiting and ceased.
This method ranks genes according to their relative difference in expression (Student's t-test) between two cell phenotypes.
Differential expression of 1,443 genes was observed between cystic and surface epithelial cells (Supplemental Table S4), suggesting the presence of distinct gene expression phenotypes in the two cell populations.
Meanwhile, the declined extent of their expression levels makes sense between two main phenotype of HSCR.
Differential expression analysis can only be conducted between two phenotypes such as tumor versus normal or treated versus untreated.
We then measured the association between LD-derived tagging SNPs with expression phenotypes.
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