Therefore, in future work we will construct new KY3 strains that can efficiently convert cellulose into component sugars by integrating more cellulolytic genes and by optimizing multiple gene expression ratios via the PGASO method.
Table 1 shows two representative genes with multiple replicates for the expression ratios of Fum/O2.
Data from multiple highly accurate gene expression ratios were combined as described previously 3, 6 by calculating the geometric mean (ie, "combined score"), (R1R2R3)1/3, where Ri represents a single ratio value.
The variability of allelic RNA expression ratios across multiple SNPs in a single gene is another metric that can guide our search for allelic expression imbalance.
To assess the observed variability in gene expression ratios, we used multiple hypothesis testing to identify genes with log2-ratios statistically significantly different from 0. The statistical analyses were based on filtered, transformed, normalized and dye-swap averaged data using a moderated t-test.
The hybridization results of the biological triplicates (i.e., treatment-vs.-treatment expression ratios) were evaluated using multiple comparison tests (ANOVA) followed by a Benjamini-Hochberg false-discovery-rate filtering procedure [ 64] provided in the Genespring 11 software package.
Multiple mechanisms are also implied by the normal distribution of the expression ratios Sor55/3153A of Ch5b genes shown in Fig. 1.
Our studies and others make it evident that RNA-Seq advances our ability to interrogate multiple aspects of the transcriptome in a single experiment, including allelic RNA expression ratios, as compared to single-gene approaches.
Taking into account the factors that best improved concordance between RNA-Seq allelic ratios and those measured by SNaPshot, we used IUPAC aligned gene-wise allelic ratios averaged at multiple annotated SNPs, leaving us with the 4,667 gene x tissue allelic RNA expression ratios, 641 of which were ≥2, as noted above.
Using analysis of variance (ANOVA) and multiple hypothesis testing, we estimated the impact of amplification on the preservation of gene expression ratios.
