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The Mouse4302 microarray was annotated by the R package mouse4302.
The MG-U74A microarray was annotated by Affymetrix platform GPL81 on NCBI.
From the genome-wide survey of zebra finch prohormones, the most commonly used zebra finch microarray platform (20K SoNG microarray) was annotated for its prohormone content [ 22].
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Transcripts identified in the microarray were annotated for GO [24] assignments using DAVID database [25].
ESTs from the microarray were annotated using BLASTX, as described [ 30] and Blast2GO [ 54, 55].
Sex-enriched genes identified in the microarray were annotated in Blast2GO v. 12.7.0 [ 44].
Only 51% of the 249 differentially expressed genes on the microarray were annotated.
Blackcurrant unigenes used to construct the microarray were annotated with the most significant BLAST homologue to Arabidopsis gene loci.
To analyze the involvement of differentially expressed genes in different biological functional groups, all the genes present on the microarray were annotated for their biological processes.
Next, we determined how many of the selected 199 differentially expressed genes are annotated at each term and how many of the genes that were assayed (all the genes represented on the microarray) are annotated at the term.
In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database.
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