A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes

Rodenburg, Wendy; Heidema, A. Geert; Boer, Jolanda M. A.; Bovee‐Oudenhoven, Ingeborg M. J.; Feskens, Edith J. M.; Mariman, E.C.M.; Keijer, Jaap

doi:10.1152/physiolgenomics.00167.2007

Cited by 45 publications

(28 citation statements)

References 45 publications

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“…Another approach to defining variable importance thresholds (to exclude truly unimportant variables) requires the training of many additional forests, where the response variable for each forest is permuted (Rodenburg et al, 2008). However, this approach is more computationally expensive than the dummy variable approach, as additional random forests must be constructed.…”

Section: Random Forest Variable Importancementioning

confidence: 99%

Interpretation of nonlinear relationships between process variables by use of random forests

Auret

Aldrich

2012

Minerals Engineering

177

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Section: Random Forest Variable Importancementioning

confidence: 99%

Interpretation of nonlinear relationships between process variables by use of random forests

Auret

Aldrich

2012

Minerals Engineering

177

View full text Add to dashboard Cite

“…Next to commercial software, open source tools are becoming available for transcriptome and metabolome networks (www.pathvisio.org). In addition to pathway tools, statistical tools that make use of interaction between genes are being employed and seem well suited for the analysis of nutritional datasets, which are characterized by multiple small effects [97].…”

Section: Challenge Tests As Biomarkersmentioning

confidence: 99%

Challenging homeostasis to define biomarkers for nutrition related health

Ommen

Keijer

Heil

et al. 2009

Molecular Nutrition Food Res

Self Cite

145

139

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A primary goal of nutrition research is to optimize health and prevent or delay disease. Biomarkers to quantify health optimization are needed since many if not most biomarkers are developed for diseases. Quantifying "normal homeostasis" and developing validated biomarkers are formidable tasks because of the robustness of homeostasis and of inter-individual diversity. In this paper, we discuss the science, strategies, and technologies for measuring parameters that define individual health. The following concepts are central to define the physiology of the healthy individual: (i) responses to a challenge of homeostasis will be more informative than static homeostatic measures; (ii) processes involved in maintaining homeostasis usually are multi-factorial and require quantitative analyses of the many individual components involved; (iii) health includes a large variation in "normality" and the effects of nutritional interventions may remain hidden in this "diversity of robustness," if incompletely analyzed. Specifically, comprehensive multi-parameter ("omics") analysis may identify key parameters (biomarkers) and lead to a greater understanding of health supporting processes. Perturbation tests that accurately target aspects of the overarching drivers of health (metabolism, oxidation, inflammation, and psychological stress) may be instrumental in creating knowledge for maintaining health and preventing disease through nutrition.

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“…Genes were considered to be regulated when meeting the criterion: absolute fold change (FC) Z1.2 and p-value r0.05. An FC of 1.2 was chosen not to overlook small changes caused by dietary intervention and more importantly to find multiple altered genes in one pathway reflecting its physiological relevance [24]. Per pathway z-score was calculated [23].…”

Section: Pathway Analysismentioning

confidence: 99%

Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

Kipp

Banning

Schothorst

et al. 2009

Molecular Nutrition Food Res

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106

112

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Selenium is an essential micronutrient. Its recommended daily allowance is not attained by a significant proportion of the population in many countries and its intake has been suggested to affect colorectal carcinogenesis. Therefore, microarrays were used to determine how both selenoprotein and global gene expression patterns in the mouse colon were affected by marginal selenium deficiency comparable to variations in human dietary intakes. Two groups of 12 mice each were fed a selenium-deficient (0.086 mg Se/kg) or a selenium-adequate (0.15 mg Se/kg) diet. After 6 wk, plasma selenium level, liver, and colon glutathione peroxidase (GPx) activity in the deficient group was 12, 34, and 50%, respectively, of that of the adequate group. Differential gene expression was analysed with mouse 44K whole genome microarrays. Pathway analysis by GenMAPP identified the protein biosynthesis pathway as most significantly affected, followed by inflammation, Delta-Notch and Wnt pathways. Selected gene expression changes were confirmed by quantitative real-time PCR. GPx1 and the selenoproteins W, H, and M, responded significantly to selenium intake making them candidates as biomarkers for selenium status. Thus, feeding a marginal selenium-deficient diet resulted in distinct changes in global gene expression in the mouse colon. Modulation of cancer-related pathways may contribute to the higher susceptibility to colon carcinogenesis in low selenium status.

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A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes

Abstract: Rodenburg W, Heidema AG, Boer JM, Bovee-Oudenhoven IM, Feskens EJ, Mariman EC, Keijer J. A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes.

Cited by 45 publications

References 45 publications

Interpretation of nonlinear relationships between process variables by use of random forests

Interpretation of nonlinear relationships between process variables by use of random forests

Challenging homeostasis to define biomarkers for nutrition related health

Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

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