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Transcription factor binding annotations were extracted from TRANSFAC.
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Another set of genes with AS annotations were extracted from the Ecgene dataset.
Gene annotations were extracted from the Ensembl BioMart database.
Functional annotations were extracted from the KO database for these 550 genes.
Equine mature miRNAs annotations were extracted from the miRBase database (http://www.mirbase.org/).org/
The mature and precursor miRNA annotations were extracted from miRBase [ 64].
The Gene Ontology (GO) annotations were extracted from the UniprotKB-GOA database [ 60].
GO terms from the Pfam annotations were extracted from the merged output file of InterProScan.
The roDROMEGa array annotations were extracted from text dump files obtained from Roche.
In these analyses, GO annotations were extracted for human proteins with known phosphorylation sites.
FlyBase gene annotations were extracted from the 29-08-2003 FlyBase genes dump file located at.
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