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Additional proteins that displayed the expected fold change included WNT16, Jumonji, TRPC5, SVCT, NOGO-A, Fbxo42, Enolase1, and Morca2a.
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values.
The Affymetrix data plotted were based on twelve to 154 data points for each expected fold change, thus representing a total of 366 data points.
There was also a strong correlation between calculated and expected fold changes in transcript expression between samples spiked with ERCC mix 1 and ERCC mix 2 (p = 1.5E-18, R = 0.6223).
Having revealed that both platforms have difficulties recovering the expected fold change for a small subset of miRNAs we speculated if these poorly recovered miRNAs were the same for both platforms.
For example, the results in Figure 2 showed a relative error ([fold change expected – fold change observed]/fold change expected) of 17% which is low compared with higher errors reported elsewhere [ 25].
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Structural modeling showed that DmCatD exhibited the expected folding for this type of enzyme, and an active site with conserved architecture.
To discuss different mechanisms of flame front disturbances according to their relevance, the flame curvature is compared with characteristic turbulence scales of the flow field and with the expected folding scale derived with Sivashinsky's formulation of linear flame instability theory.
In the absence of known or expected fold-change values in this data set, it is not possible to assign greater accuracy to any of the methods.
This time, as expected, fold-recognition analysis of a well-defined protein core gave unambiguous results: mGenTHREADER, SPARKS, and FUGUE reported structures of Holliday junction resolvases Hjc and Hje, members of the PD-(D/E XK fold [ 7- 9], at the first positions of their rankings, with significant scores (0.45, -2.08, and 3.46, respectively).
Here careful design of the artificial sequences taking into consideration the expected folding, especially the drosha and dicer cut sites, may be required.
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