2008
DOI: 10.4137/cin.s791
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Efficiency Analysis of Competing Tests for Finding Differentially Expressed Genes in Lung Adenocarcinoma

Abstract: In this study, we introduce and use Efficiency Analysis to compare differences in the apparent internal and external consistency of competing normalization methods and tests for identifying differentially expressed genes. Using publicly available data, two lung adenocarcinoma datasets were analyzed using caGEDA (http://bioinformatics2.pitt.edu/GE2/GEDA.html) to measure the degree of differential expression of genes existing between two populations. The datasets were randomly split into at least two subsets, ea… Show more

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Cited by 25 publications
(28 citation statements)
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References 37 publications
(69 reference statements)
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“…Differential methylation was determined using intelligent methods optimization by Efficiency Analysis [30]. This approach selects the most reproducible combination of transformation, normalization, test for differential coverage, and a learned threshold of significance via resampling.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…Differential methylation was determined using intelligent methods optimization by Efficiency Analysis [30]. This approach selects the most reproducible combination of transformation, normalization, test for differential coverage, and a learned threshold of significance via resampling.…”
Section: Discussionmentioning
confidence: 99%
“…Methylation of coding gene sets were calculated from .bam files as average coverage of the total sum of exons represented in a canonical protein coding locus, and methylation of non-protein coding annotated genes were represented by the average coverage of the annotated locus. Calculations of average coverage utilized RNASequnator software [30].…”
Section: Discussionmentioning
confidence: 99%
“…The researchers concluded that DAT expression in males undergoes larger decreases after injury, compared to females, but EE exposure has larger effects on postinjury DAT expression in females versus males. 137 Shin and colleagues 138 characterized the mRNA expression profile in substantia nigra (SN) and ventral tegmental area (VTA) at 4 weeks postinjury alone and in combination with enriched housing by using efficiency analysis of microarray data 139 to assess differential gene expression. Aside from alterations in genes involved in inflammation and cellular plasticity, there were also chronic alterations in genes important for calcium and DA signaling pathways in TBI animals exposed to EE, such as down-regulation of tyrosine hydroxylase and up-regulation of alpha-synuclein, which may represent compensatory mechanisms to counteract the detrimental effects of TBI.…”
Section: Potential Mechanisms For Environmental Enrichment-induced Bementioning
confidence: 99%
“…Calculation of average coverage utilized RNASequnator software [16]. Differential methylation was determined by optimized means using Efficiency Analysis [17] which selects the most reproducible combination of transformation, normalization, test for differential coverage, and a learned threshold of significance via resampling. The result is selection of a low-bias measure of differences in average coverage between group-wise comparisons between experimental and control data sets.…”
Section: Discussionmentioning
confidence: 99%