Loci that do not match any previously annotated genes are tagged as de novo.
A total of 5,483 transcripts (23.9%) had a complete match to previously annotated transcripts, while 17,406 (76%) were potentially novel.
A total of 10285 transcripts were identified, of which 1884 did not match with previously annotated genes and therefore were categorized as novel genes.
We identified 9,286 novel transcripts that completely matched the previously annotated intergenic regions of the genome.
Annotation of the 6424 non-redundant root transcripts revealed 4505 (70%) had known functions, 455 (7%) matched a previously annotated gene model, but the function was unclear, and 1464 (22.8%) had unknown functions, with no homology matches to any previously described gene.
The initial steps of the pipeline identified sequence matches to databases of previously annotated RNAs (e.g., known miRNAs, other noncoding RNAs, messenger RNAs) and to highly repetitive sequence elements.
DOI: http://dx.doi.org/10.7554/eLife.03346.011 De novo motif analysis using 50 bp around the ZEB1 peak summit revealed a top-scoring motif that strongly matched MA0103.2 (TOMTOM p=10−8), which was previously annotated as the ZEB1 position weight matrix (PWM) in Jaspar (Gupta et al., 2007).
All spectra were searched against these ORFs, and after omitting the single hits, 186 ORFs remain (Additional File 1) that can be divided into two groups: "Group A" being matched by both pre-existing and new peptides, i.e. corrections of previously annotated proteins, and "Group B" being matched only be new peptides, i.e. novel proteins.
ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry.
