There were multiple unique putative transcripts for genes in this pathway, including transcripts encoding cinnamate 4-hydroxylase, chalcone synthase, chalcone isomerase, NAD(P H-dependent 6'-deoxychalcone synthase and flavonoid 3',5'-hydroxylase (F3'5'H) (see Additional file 2).
The molecular diversity of 3FTx genes of MOh is well reflected by the presence of multiple unique 3FTx transcripts.
Whether the multiple or unique transcripts of miRNA have a special function is still unknown.
Use of multiple unique probes per transcript in general increases the confidence of microarray result.
Reads mapping to overlapping regions between multiple transcripts were assigned to unique transcripts based on information from the uniquely mapping portion of each transcript and by assuming an additive effect of the read depth in the overlapping regions.
Tiling arrays also optimize the detection of viral genes by using multiple unique probes for one transcript, an advantage over low-density spotting arrays or individual primer/probe sets used for PCR-based detection.
By comparing annotated transcripts from different assemblies of the T. biloba transcriptome, we demonstrate that our pipeline recovers a greater number of transcripts than standard approaches by pooling unique transcripts from multiple assemblies.
It is therefore more informative to examine unique transcripts (ie. counting multiple transcripts for the same gene only once) rather than total transcripts.
This finding suggests alternative pathways for the regulation of these unique transcripts, which may involve multiple scenarios of cross-talks between hypoxia and NO operating in inflammation or cancer.
Using this approach one can identify unique transcripts as target sequences, design multiple oligo probes per target, test and select the optimal and unique oligo probes, and annotate the final selected probed target sequences.
