Rather than generating sequence reads from transcripts, we only used exons of genes with two exons.
Importantly, genes with two CCAAT boxes, predicted to be down-regulated by CDP, were found underexpressed in the latter group.
CTCF knockdown [33] affects three of these genes, with two of them being repressed and one being induced (Table 1).
To compute fc we have ignored the genes with only one regulator, taking into account only the 817 genes with two or more regulators.
Therefore, we evaluated correlation between the fold changes obtained from redundant probe sets, focusing as before on genes with two redundant probe sets (Table 3).
The C. remanei genome has three gene pairs that are homologous to the C. elegans genes with two pairs in the same contig.
It should also be noted that for some genes with two or more proximal lethal P-elements, only one was found to cause a LT+ phenotype (Table S1).
For example, genes with two redundant probe sets assigned by Affymetrix grouping showed inconsistent P/A calls in 31% of the genes.
To further examine the relationship among P/A calls, significant probe sets, and consistency of the redundant probe sets, we examined in detail the genes with two probe sets.
Among genes with AP, there are 3, 772 genes with two promoters (AP = 2), 2,941 with three or four (AP = 3∼4), and 1,176 with five or more (AP> = 5).
For instance, according to the regulonDB, which gives the topology of the transcription regulatory network of E. coli [46], there are at least 817 genes with two or more regulators.
