Specifically, we first focused on the best-annotated songbird species, the Zebra finch, retrieving all Zebra finch Ensembl gene models annotated as novel, duplicated, or expanded (>7,000 models, e59), and removing models Ensembl considered to have orthologs in other species (n = 5,459), as well as those mapped to chromosome Unknown (n = 1,179), which were likely to represent allelic variants.
The first set consisted of the set of Ensembl models annotated as Uncharacterized Proteins with a status of 'Novel' in Zebra finch.
Other miRNA targeted genes include cDNA models annotated as auxin response factor, HD-zip transcription factor, and Ap2-like transcription factor.
Of 39 transcript models annotated as sulfate transporters, 22 were upregulated between stages C-I and C-II in cotyledons, and 14 were significantly upregulated in leaf tissues, and eleven of these were common to both sets.
Among all tissues and treatments examined, 5,156 unique genes were classified as DE (Additional File 4); including 5,018 high confidence and 123 low confidence protein-coding genes, and 15 models annotated as pri-microRNAs [ 43].
We identified this set by retrieving the complete set of protein-coding models in Zebra finch from Ensembl BioMart (ensembl.org/biomart/martview), and excluding all models annotated as "Known", models with orthologs in other species, and models placed onto 'chromosome Unknown', which are thought to largely represent allelic variants.
BLAST searches with the cDNA sequence X77015 corresponding to the differential Lap protein against the potato genome sequence [ 30] identified superscaffold PGSC0003DMB000000116 (chr12:910581..2552409), which contained a single gene model annotated as 'neutral Lap' (StLapN).
We noted that the reference genome sequence (Eichinger et al., 2005), derived from the axenic mutant strain AX4, also differs from its parent DdB in the same gene model (annotated as DDB_G0279251).
Contigs were annotated as above.
We use the performance analysis techniques developed previously in the PUMA project, which take as input UML models annotated with the standard UML Profile for Schedulability, Performance and Time (SPT), and transform them first into Core Scenario Model (CSM), and then into different performance models.
BioModels web services [ 27] provide several methods that can be used to retrieve all models annotated with commonly used resources such as GO, UniProt, Taxonomy, ChEBI and Reactome.
