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Immunization-induced transcriptional regulation of 300 of these 1,266 genes was restricted to Treg as indicated by an expression ratio of 0.75 1.25 between splenic conventional T cells (Tconv) from immunized and naive mice (red dots in Fig. 2b).
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All genes returned by ANOVA had an expression ratio larger than two.
Moreover, all genes returned by ANOVA had an expression ratio equal/larger than two, indicating the power of the analysis.
Rab11, also developmentally regulated [ 15], gave an expression ratio below 2.5 by both limma and fspma analysis.
Results obtained by default analysis and derived from 'A'/'C' expression ratio for 25,955 loci (Additional file 8) included 2 significantly over-expressed segments in DS AMKL (Table 6a).
Another indicator of early OA, as demonstrated by animal models of OA and in OA patients, is increased bone remodeling characterized by a decreased expression ratio of OPG to RANKL[ 29, 30].
If so, this may have several causes, like a lower degree of kinase modulation by light, or a suboptimal expression ratio of the proteins composing the light-responsive signal transduction pathway.
We subsequently analyzed this gene set by hyperclustering, a technique that allows the data to be clustered by both expression ratio and gene annotation (e.g. Gene Ontologies).
For the former searches, the input data can be gene-expression signatures represented by a set of genes with up- or down-regulated labels or by gene expression ratio data.
fold change, defined by the expression ratio of cancer to normal (= cancer/normal) All these genes had false discovery rate <0.001.
Microarray data were ranked by the expression ratio between the geometric mean of the CD24−/low/CD44+ CD24+/CD44+ populations from the three cell lines (Supplementary Table).
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