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Several comparison analyses were performed using Pearson's chi-square test.
Combining the SS shared across several comparison analyses, a total of 42 regions were identified with 125 genes related to these genomic positions (see Additional file 1).
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Given that complex regulatory networks in stem cells can be best detected by expression analysis of many genes, we performed several gene set comparison analyses comparing our acquired resistance signatures with published ES cell signatures as reported by Ben-Porath et al13 (Table S6).
As such, and motivated by the concerns of the reviewer regarding the reliability of the bilateral FOF fits, we have added several extra model comparison analyses to the paper.
To generate a user-defined gene set for our gene comparison analyses, we adopted several gene lists from the published work of Ben-Porath et al [13], in which several gene sets associated with ES cell identity were compiled for gene set comparison analyses.
GSA, Gene Set Expression comparison Analyses; RE, Regulatory Effect We explored several aspects of the association of the miRNA target genes with outcome.
RubS DNA sequence comparison analyses by ClustalW.
RubL DNA sequence comparison analyses by ClustalW.
Comparison analyses were performed using logistic regression.
9 Simple comparison analyses and mixed models analyses were applied.
Logistic regression analyses were performed in several comparisons where the men were divided in risk groups according to the risk points in the health profile (table 1).
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