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The GC-dependent transcriptome was defined by differential expression between the intermediate- and low-CORT groups.
Gene lists are ranked by differential expression between two classes, compared in microarray experiments [ 11- 16].
We compared this with simply ranking the transcription factors by differential expression between the "transforming" viral gene samples and the control samples.
More recently, Gorlov et al. [ 69] found that the top genes by differential expression between normal and cancer tissue from human prostate are enriched for the same functional categories as the top candidate genes in GWAS and that strength of association in both tests was correlated.
We used a Rank Product analysis for the public studies, which considered only the ranking of genes by differential expression between pairs of samples within studies [ 20, 30], avoiding batch and platform-related effects which would occur from directly combining expression values from the different studies.
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We first identify a set of tumor suppressors and oncogenes by differential expression analysis between the cancer and control groups.
In general, genes that are differentially expressed can be identified by determining differential expression between treatments.
For instance, a frequently applied method is to score genes by their differential expression between two biological states (such as healthy vs. diseased).
Our data supported the imprinted status of HOXA4 at 7p15.2, GLI3 at 7p13, and SVOPL at 7q34 by showing differential expression between matUPD7s and patUPD7 and a significant expression difference between matUPD7s and controls.
To this end, the tumour samples were divided into three groups of the same size according to their CD95 expression (high, intermediate and low), and preranked genes by their differential expression between CD95 high- and CD95 low-expression samples.
By comparing differential expression between the bulk of cancer cells and cancer stem cells, we have identified a group of candidate genes that might be essential for growth and survival of cancer stem cells [ 46].
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