Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs.
Real time variables were analysed by generation of the mean threshold cycle (CT) value for each transcript in duplicate.
This 715-transcript dataset contained 48 duplicate transcripts, yielding 667 unique transcripts which correspond to 437 unique genes for subsequent GOMiner analyses.
A specific standard curve was performed in parallel for each gene to assess the specificity of the products, for quantification of the respective transcripts in duplicate.
Because siRNAs can have off-target effects, we used two independent PML siRNAs ("siP1" and "siP2") targeting different regions of PML transcripts with duplicate samples to help eliminate false target genes.
This list was obtained by comparing profiles of genes detected by the three treatments, excluding duplicate transcripts, unknown transcripts and transcripts not detected in one or two of the treatments.
We filter out duplicate transcripts (transcripts sharing exonic coordinates and thus differing only in the locations of their untranslated regions) and alternative haplotype/supercontig entries from the cDNA sequences and the genome assembly.
This is to be expected since gene duplication events are likely to involve "upstream" regulatory DNA, and so transcripts of duplicated genes are likely to be co-regulated.
However, we cannot rule out that changes in the expression of parent-specific transcripts or duplicates may have occurred more or less frequently in specific functional categories, since our microarray could not measure this.
This is true also for C. hamatus mapped transcripts, because duplicated genes were identified and counted inside each subtree.
We individually reviewed each of the initially identified articles and transcripts, discarding duplicates or non-relevant articles.
