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This list of target genes was then subjected to KEGG analysis using the DAVID online functional annotation tool [ 27].
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This list of targeted genes includes genes requested by members of cotton research community, a large number of transcription factors, and several thousand genes that had homology to Arabidopsis genes (Table 1) [see Additional file 1].
The test was considered successful if the TF referenced in TRED as regulating this list of targets was retrieved among n candidates having the highest scores for coverage or for specificity.
This list of targets includes ADO1, FYV8, GET2, HAC1 and IRE1, all of which have been shown to be sensitive to tunicamycin when knocked out, as well as BCK1, a gene which has previously been shown to be resistant to tunicamycin when overexpressed [ 19, 21- 24].
However, this mutation was not in the list of target SNPs (Additional file 1).
For the list of target promoter primer pairs see supplementary materials.
The first selects random candidate genes as before, but retains the list of target genes.
Interestingly, with the exception of Fas, this list of p53 target genes consisted predominately of genes encoding proteins involved in cell cycle arrest or DNA repair.
As above, we used IPA to predict mRNA targets for these stably expressed miRNAs and compared this list of predicted targets with the differentially expressed mRNAs identified through mRNA transcriptome profiling on BeadChips.
We predicted target genes for these nine candidate miRNAs using TargetScan software and analyzed gene pathways enriched in this list of predicted targets using the PANTHER gene ontogeny database.
He said only five or six countries have the capabilities to wage a cyberspying mission of this scale, but the list of targets reflects the interest of China more than any other country.
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