A second dataset, hereafter annotated as Abiotic, contains replicated analysis of Arabidopsis thaliana transcriptional response to multiple abiotic stresses [34].
> -wrap-foot> We then annotated protein-coding regions (hereafter referred to as "genes" unless otherwise indicated) from the transcriptome assembly.
All analysis hereafter refers to the annotated RefSeq genes.
Human BCRP [UniProt: Q9UNQ0] inhibition data was composed of data from the Open PHACTS Discovery Platform [3, 22] and of manually annotated data collected from literature sources [15], hereafter called pre-curated data.
In our analysis we annotated both contigs and singlets after assembly (hereafter referred as transcripts), since they contained different sequences and relevant information.
We trained TEES in a gold-standard set of 20 full text annotated documents, 10 on human embryonic stem cell research (hereafter called CF-hESC), whose entities annotations have been previously published (46) and a new set of 10 full texts documents on kidney stem cell research (hereafter called CF-Kidney).
Using a stringent threshold (p < 0.005; see Methods) we found 6.8% (1,177) of coding RefSeq transcripts to be associated with long upstream antisense transcripts (hereafter, LUATs), of which 236 overlap with previously annotated non-coding transcripts.
Thus, we found a potential genome copy of a full-length LINE retrotransposon with 2 ORFs (that we hereafter name Kryze) in a full-length genome copy annotated by TE consensus Bgh_RIX_G4472 (81.5 % of nucleotide identity), extended to 3000 bp downstream.
We performed a series of BLAST searches to establish homology between contigs or singletons (both referred to hereafter as "ESTs") from Ae. albopictus and annotated genes from other organisms.
With the exception of the genes in the segmentally duplicated category which, by definition, have a pre-determined parent, parent genes were identified by alignment of the 16,284 fully-supported genes annotated in Osa1 Release 5 to the genomic sequence of the GPFs, hereafter referred to as Locus Targeted for Investigation (LTIs, see Additional file 2).
