Two transcript profiles ('y' and 'z') were based on a computationally generated transcript profile ('x'), forming a small artificial network with edges between the nodes x and y in addition to x and z.
The three proteomes correlated much more weakly with each other (0.59-0.75, table 1, C) than did the three transcriptomes, indicating greater differences between the protein profiles than between the transcript profiles.
The edges between the nodes indicate only actual relations (based on partial correlations) between transcript profiles.
We found no associations between gender and transcript profiles.
However, previous research involving cross-species hybridization (CSH) has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected) and the accuracy of measuring fold-differences in gene expression.
Since it is still very difficult to isolate zygote and two-celled proembryos from Arabidopsis and we have well established relevant techniques in tobacco [3], [12], in this report, we present a comparison of the transcript profiles between the two zygotic daughter cells of tobacco, and we compare the two cell types with the zygote.
Since this is EST-based and sampling analysis, the diversity of the transcript profiles between the two cell types needs to be further confirmed.
Monitoring and comparing transcript profiles between the two phases from various developmental stages showed a sharp rise in phase differences during the 4th instar and then maintained those levels in all following stages (Figure 3 and Figure S7).
Comparative analysis with A. thaliana embryogenesis also highlighted genes involved in auxin-mediated responses, as well as epigenetic regulation, indicating highly correlated transcript profiles between the two species.
To compare transcript profiles between the two species, the fold-changes in transcript levels at each stage versus the average value throughout embryogenesis in each species was quantified for each data series.
