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Remarkably, the six transcriptional networks under the control of PhoP identified in this work appears differentially expressed in response to macrophage infection (Table S1), indicating that PhoP might control key functions for intracellular survival.
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For example, if only one of a set of redundant probe sets appears differentially-expressed, should this lessen confidence that the gene itself is changed in response to the treatment being investigated in an experiment?
Among all candidate floral homeotic genes tested, only RhAG appeared differentially expressed between 'Malmaison' and 'St Anne's' (Figure 5A).
In order to simplify the analysis, we focused on those genes that appeared differentially regulated in at least two of the four microarrays (Table S1 and S2).
Instead of selecting genes from susceptible diabetic risk loci, we have considered all those genes that appeared differentially expressed in our analysis.
In such infected host tissues, approximately 15% (n = 211) of the total predicted R. conorii ORFs appeared differentially expressed compared to bacteria grown in standard laboratory conditions.
To correct for multiple testing, we estimated the false discovery rate (FDR) at p<0.01 to be 0.52, thus, at the considered cutoff we would expect 107 transcripts to appear differentially expressed solely by chance (compared to the 204 differentially expressed transcripts observed).
Specific intervals of a broad complement of TE families appear differentially expressed in any given tissue.
Interestingly, p62 protein appeared differentially localized in Atg7 and Vps15 mutants.
GeneSpring analyses identified 202 annotated genes that appeared differentially expressed at least at one sampling time (P < 0.05).
Other transcripts only appeared differentially expressed in one of the arrays, such as il17 d and il22 (Table 2).
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