The full data set of Beissbarth et al actually comprises more than 367 regulated transcripts many of which are only identifed as ESTs.
Interestingly, at 48 h, there were far more down-regulated transcripts than up-regulated transcripts for the 4 compounds 2,4DNT, 2,6DNT, 2ADNT, 4ADNT.
TNT showed a reverse trend once again in that it induced more up-regulated transcripts at 48 h than down-regulated ones.
According to this criterion, we found another common phenomenon: there were much more up-regulated transcripts than down-regulated transcripts at 24h and both time points together (24 h+48 h) (Figure 5) for 2,4DNT, 2,6DNT, 2ADNT, 4ADNT and TNT.
CC and M21 showed very similar patterns of up-regulation although the number of genes observed in each category was slightly higher for M21, with the exception of "abiotic stress genes" where more up-regulated transcripts were observed for CC.
In addition, there were more down-regulated transcripts (LPL and BLP) than up-regulated transcripts (AHP and HPL) at the tillering stage.
More down-regulated transcripts than up-regulated transcripts were identified during the transition from L5D6 to PP and from PP to P0.
For example, if a gene has more up-regulated transcripts than down-regulated ones, then it is considered as up-regulated.
When gene expression between genotypes in both tissues was compared, there were consistently more up-regulated transcripts than down-regulated ones (Table 2 and Fig. 7 A ).
Among the DEGs, there were more up-regulated transcripts than down-regulated ones, indicating that many genes responded positively to ABA treatment.
