Filtering for increased power for microarray data analysis

Hackstadt, Amber J.; Hess, Ann

doi:10.1186/1471-2105-10-11

Cited by 246 publications

(232 citation statements)

References 11 publications

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“…Integrated peak height intensity was tabulated for 700 negative ion mass features (Dataset S1) and 1,164 positive ion features (Dataset S2). Data filtering removed 25% of the negative features and 40% of the positive features before analysis (37). Principal component analysis (PCA) showed that maximum variation in global metabolite pools was between individual ears independent of kernel genotype (Fig.…”

Section: Resultsmentioning

confidence: 99%

Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

Lappe

Baier

Boehlein

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the large majority of endosperm PPDK, whereas pdk1 specifies the abundant mesophyll form. The pdk1- mutation is seedling-lethal, indicating that C4 photosynthesis is essential in maize. RNAi expression in transgenic endosperm eliminated detectable PPDK protein and enzyme activity. Transgenic kernels weighed the same on average as nontransgenic siblings, with normal endosperm starch and total N contents, indicating that PPDK is not required for net storage compound synthesis. An opaque phenotype resulted from complete PPDK knockout, including loss of vitreous endosperm character similar to the phenotype conditioned by o2-. Concentrations of multiple glycolytic intermediates were elevated in transgenic endosperm, energy charge was altered, and starch granules were more numerous but smaller on average than normal. The data indicate that PPDK modulates endosperm metabolism, potentially through reversible adjustments to energy charge, and reveal that o2- mutations can affect the opaque phenotype through regulation of PPDK in addition to their previously demonstrated effects on storage protein gene expression.

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Section: Resultsmentioning

confidence: 99%

Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

Lappe

Baier

Boehlein

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Sequences were also assigned to phylotypes using the phylotype command in Mothur. A multivariate data analysis of the OTUs was performed using METAGENassist (Arndt et al, 2012), followed by normalization based on interquantile range (IQR) (Hackstadt and Hess, 2009) and log 2 -transformation. IQR normalization allows one to increase statistical power by removing sequences that do not fall within the middle 50% of observations and thus reducing the number of statistical tests one has to perform.…”

Section: Methodsmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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“…In the microarray literature, several authors have suggested filtering to reduce the impact that multiple testing adjustment has on detection power (7)(8)(9)(10)(11)(12). Conceptually similar screening approaches have also been proposed for variable selection in high-dimensional regression models (13,14).…”

mentioning

confidence: 99%

Independent filtering increases detection power for high-throughput experiments

Bourgon

Gentleman²,

Huber

2010

Proc. Natl. Acad. Sci. U.S.A.

648

633

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With high-dimensional data, variable-by-variable statistical testing is often used to select variables whose behavior differs across conditions. Such an approach requires adjustment for multiple testing, which can result in low statistical power. A two-stage approach that first filters variables by a criterion independent of the test statistic, and then only tests variables which pass the filter, can provide higher power. We show that use of some filter/test statistics pairs presented in the literature may, however, lead to loss of type I error control. We describe other pairs which avoid this problem. In an application to microarray data, we found that gene-by-gene filtering by overall variance followed by a t-test increased the number of discoveries by 50%. We also show that this particular statistic pair induces a lower bound on fold-change among the set of discoveries. Independent filtering-using filter/ test pairs that are independent under the null hypothesis but correlated under the alternative-is a general approach that can substantially increase the efficiency of experiments.gene expression | multiple testing

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Filtering for increased power for microarray data analysis

Cited by 246 publications

References 11 publications

Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm

Rhizosphere microbiome assemblage is affected by plant development

Independent filtering increases detection power for high-throughput experiments

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