In agreement with this prediction, duplicated genes had on average more total eQTL per transcript than the unique genes or the whole genome average (Figure 3A).
Out of these 249 GOs, only those GOs have been plotted which accounted for more than 10%% of total transcripts (Additional file 3: Figure S2).
Consistent with previous studies, loss of H2A.Z deposition (swr1Δ) had little effect on steady-state transcript abundance compared to wild-type (WT) (Mizuguchi et al., 2004), as no transcripts were reduced 1.5-fold or more from the 7,987 total transcripts monitored at a stringent criterion of false discovery rate (FDR) < 0.1.
As anticipated, more probes were found to match to AceView transcripts than RefSeq transcripts, with 21%, 11%and13%3% more total probes for Agilent, Codelink and Affymetrix, respectively.
This figure signifies the dominance of biological process followed by metabolic process as GO categories to which the maximum number of transcripts were mapped i.e. more than 80% and 600 %, respectively, of the total transcripts from the microarray data.
More than half of the non matching spruce transcripts (9.8% of the total transcripts) were indeed derived only from 3' reads.
It is therefore more informative to examine unique transcripts (ie. counting multiple transcripts for the same gene only once) rather than total transcripts.
For example, the centrally located, UpsC starter gene var29 in culture #8 accounted for more than 90% of the total transcript level at the first measurement and remained the dominant variant over the following 60 generations.
We found that 2,541 (15.56% of total) transcript families contained more than 20 members, with the largest family containing 2,724 isoforms.
However, the overall regulation intensity (% regulation of scored vs. filtered transcripts) appeared to be more similar between 12 00 and 15:00, which was in agreement with the similar level of total transcript regulation at both times of day (cf. Fig. 1).
