Little is known about silencing of SIN lentiviral vectors in ES cells but it has been shown that transgenes are efficiently expressed at multiple copy integrations but single copy integrations results in inconsistent expression [12], [13], [23], [28].
After eliminating transcripts that displayed inconsistent expression levels throughout the time course, such as those that were not expressed at high enough levels for meaningful analysis (see Materials and Methods for details), we were left with 6956 genes (File S3).
Further, for GAPDH, inconsistent expression among the tissues and hypoxic time periods was observed.
The expression of PaSPL was complementary to the expression of miR156, whereas PaAP2 demonstrated inconsistent expression patterns (Figure 7C).
If high classifier robustness or the detection of genes with inconsistent expression are a main goal, the sensitivity cutoff may be relaxed, trading classifier performance for improved resistance to noise, and a low false positive rate for improved detection of inconsistent aberrant expression.
After filtering out genes with inconsistent expression, a combination of a permutation method (SAM) and descriptive quantitative ranking of fold changes was found to be the most appropriate statistical analysis.
At 60 and 96 hours after PCNA RNAi, the pattern of expression of almost all apoptosis-related genes in isolated oocytes (Fig. 6F) was almost identical to that in PCNA RNAi ovaries, whereas only a slight and inconsistent expression of these genes was detected in somatic cells (Figs. 7C, D).
Even the segmental duplicated gene pairs had inconsistent expression profiles.
Genes with inconsistent expression patterns among different datasets were excluded from further analysis.
All putative tissue-preferred genes with inconsistent expression patterns among the four datasets were excluded for further analysis.
