Of these, Boc demonstrated the greatest degree of transcript enrichment in EP adipocytes vs. SC adipocytes.
This degree of transcript diversity has not been found in mammalian homologs of Dscam.
The representativeness of the libraries was confirmed by the high degree of transcript diversity (diversity index ranging from 60 to 75%).
Exon analyses revealed 60 hypoxia-regulated AS events with splice indices (SI) >1.0 from 53 genes and a correlation between high SI and degree of transcript regulation.
Although it remains unclear as to the degree of transcript shortening that occurs, it should be acknowledged as it may prevent construction of full length transcripts as discussed by Huang and Khatib [ 28].
These differences likely reflect the greater degree of transcript redundancy in the Oases transcriptome assembly, and together, indicate that the Trinity assembly, for the present dataset, was of higher quality for transcript expression analysis.
Transcript abundance bias was not evident in the optimal starting amount (200 ng total RNA) of the amplification protocol and we found the degree of transcript representation in the resulting aRNA pool with respect to the initial total RNA transcript population to be satisfactory for the use in gene expression analysis.
The disparity in the degree of transcript abundance regulation between T. cruzi and the other sequenced kinetoplastids suggests there may be differences in the number and kind of RNA binding proteins in their genomes, because almost all regulation of mRNA abundance in these organisms is at the level of mRNA stability.
To facilitate a functional comparison of the three major stages of berry development, Unigenes from each of the profile groups were regrouped into the three major developmental phases to reflect the greatest degree of transcript abundance changes at each phase: Phase I (profiles 1, 2, and 3), Phase II (profiles 4, 5, 6, 12, 13, and 14), and Phase III (profiles 7, 8, 9, 10, 11, 15, and 16).
Bimodality implies a high degree of transcript-level regulation, and bimodal genes may act as switches for the direction of signals and/or metabolic flow.
