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For instance, among the known set of genes, we found PHO1, PHO1 H1, DGD1, and PHF1 to be specifically regulated in response to Pistarv.
Normalized to the total number of the genes profiled in this study (12063), 17.24% and 11.75% of the genes were found to be specifically regulated in Pima and TM1, respectively, while 7.15% of the genes were regulated in both species.
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Of the 2324 hypoxia-regulated transcripts, most are specifically regulated in just a few brain regions.
Among the four Heat-stable protein1 (HSP1) up-regulated in roots, eugene3.00101442 was specifically regulated in Carpaccio.
One hundred sixty of these DEGs were specifically regulated in susceptible seedlings, 114 genes of them up-regulated with fold changes up to 336 (Additional file 4: Table S7) and 46 genes down-regulated with fold changes down to −15 (Additional file 4: Table S8).
A detailed view of the sen1 transcriptome identified several genes (537 IDs), which were specifically regulated in this genotype.
Since many C. jejuni genes are specifically regulated in vivo [31], we sought to compare transcript abundance of wild-type and mouse-adapted bacteria during mouse infection.
The majority of these genes (184 IDs) were specifically regulated in the nfr1 mutant and only 4 genes were also regulated in wild-type (Figure 2C and Folder S3).
Changes in transcription in a direction characteristic of responses to low iron were excluded from the analysis directed at identifying genes that are specifically regulated in response to each of the iron donors.
In a similar manner, genes that required ATM activity to establish the correct direction and timing of expression or were specifically regulated in atm (Fig.7 right side) were hypothesized to include targets regulated by other posttranslational regulators acting more upstream or downstream of ATM/ATR and/or further away from DSB sites, such as Tip60 and ARP4.
Identification of many genes, which are specifically regulated in the nfr1 mutant in response to M. loti inoculation, may reflect an independent function that is altered in the absence of NFR1 or alternatively, that NFR1 may control this gene set independently.
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