The framework was then applied by a research assistant to the remaining transcripts.
As remaining transcripts were coded, new codes were added or codes collapsed based on consensus of the 4 researchers.
All remaining transcripts expressed above background level in both conditions are considered similarly expressed.
The remaining transcripts either did not have either a start or stop codon or no clear ORF (Figure 6).
To reveal the most frequently occurring hexamers in the remaining transcripts, the TEIRESIAS algorithm [20] was used.
The remaining transcripts without one of the two PAS were screened for common hexamers using the TEIRESIAS-based pattern discovery tool.
The HuR binding sites of the remaining transcripts were all (at least partially) located in double-stranded regions (Fig. 4b) and therefore possibly inaccessible to HuR.
The remaining transcripts were not differentially expressed.
The remaining transcripts were possible novel lincRNAs.
The remaining transcripts exhibited partial ORFs.
The remaining transcripts were then analysed using the agreed themes.
