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As expected, the dcl1 and hen1 mutants had a high number of shared transcript changes [3], [41].
For each trait pair we searched for a potential shared transcript that showed the best correlation (on average) with both traits.
We retain a predicted transcript as a predicted shared transcript if it appears both as a query with BLAST hits from one direction and as a subject BLAST hit in the other direction.
By investigating the fitness of the alignment between the predicted shared transcripts and the known transcriptome database sequences, Figures 5 and 6 show that with respect to the accuracy of shared transcript reconstruction, there are tradeoffs between precision and recall by Mutual when compared to Oases.
Fig. 2 Shared transcript regulation between different day times of administration.
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Of the total of 5588 IGR, only 568 (10.2%) shared transcripts from both flanking ORF within the same window of peak temporal transcription during the IDC.
The dose response relationship for the expression level of the 130 shared transcripts exhibited different patterns (Figure 3).
Among the 130 shared transcripts, 12/34 transcripts normally expressed in mouse thyroids and 31/96 transcripts for which gene expression has not yet been determined in normal mouse thyroid were down-regulated after exposure to 1.4 Gy but up-regulated after exposure to 0.05, 0.5, 11, and 32 Gy (Figure 2).
The situation is different when considering predicted shared transcripts that are close to full length.
Each developmental stage was assembled separately and shared transcripts were collapsed using Cuffmerge [ 23].
DS led on analysis and met with MF and JB regularly to discuss shared transcripts.
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