Factor Analysis for Multiple Testing (<b>FAMT</b>): An<i>R</i>Package for Large-Scale Significance Testing under Dependence

Causeur, David; Friguet, Chloé; Houée-Bigot, Magalie; Kloareg, Maëla

doi:10.18637/jss.v040.i14

Cited by 14 publications

(20 citation statements)

References 17 publications

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“…These variables were gathered in a matrix made of independent observations. In order to favor strong correlations, the R package FAMT (Causeur et al 2011) was used with a FDR value of 0.01. This approach proved its usefulness in previous ecotoxicology studies (Baillon et al 2015).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Bertucci

Pierron

Thébault

et al. 2017

Environ Sci Pollut Res

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The freshwater pearl mussel Margaritifera margaritifera is one of the most threatened freshwater bivalves worldwide. In this study, we aimed (i) to study the processes by which water quality might affect freshwater mussels in situ and (ii) to provide insights into the ecotoxicological significance of water pollution to natural populations in order to provide necessary information to enhance conservation strategies. M. margaritifera specimens were sampled in two close sites located upstream or downstream from an illegal dumping site. The renal transcriptome of these animals was assembled and gene transcription determined by RNA-seq. Correlations between transcription levels of each single transcript and the bioaccumulation of nine trace metals, age (estimated by sclerochronology), and condition index were determined in order to identify genes likely to respond to a specific factor. Amongst the studied metals, Cr, Zn, Cd, and Ni were the main factors correlated with transcription levels, with effects on translation, apoptosis, immune response, response to stimulus, and transport pathways.However, the main factor explaining changes in gene transcription appeared to be the age of individuals with a negative correlation with the transcription of retrotransposon-related genes. To investigate this effect further, mussels were classified into three age classes. In young, middle-aged and old animals, transcription levels were mainly explained by Cu, Zn and age, respectively. This suggests differences in the molecular responses of this species to metals during its lifetime that must be better assessed in future ecotoxicology studies.

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Section: Methodsmentioning

confidence: 99%

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Bertucci

Pierron

Thébault

et al. 2017

Environ Sci Pollut Res

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“…By using this test, we also controlled the False Discovery Rate (FDR) over the set of contigs for a given variable. The R package FAMT (Causeur 2011) allowed us to produce a p value between a factor and contigs. For every studied variables, we then introduced two thresholds d i,1 and d i,2 and we selected a contig according to the two thresholds.…”

Section: Statistical Analysesmentioning

confidence: 99%

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels

et al. 2014

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Identifying specific effects of contaminants in a multi-stress field context remain a challenge in ecotoxicology. In this context, ''omics'' technologies, by allowing the simultaneous measurement of numerous biological endpoints, could help unravel the in situ toxicity of contaminants. In this study, wild Atlantic eels were sampled in 8 sites presenting a broad contamination gradient in France and Canada. The global hepatic transcriptome of animals was determined by RNA-Seq. In parallel, the contamination level of fish to 8 metals and 25 organic pollutants was determined. Factor analysis for multiple testing was used to identify genes that are most likely to be related to a single factor. Among the variables analyzed, arsenic (As), cadmium (Cd), lindane (c-HCH) and the hepato-somatic index (HSI) were found to be the main factors affecting eel's transcriptome. Genes associated with As exposure were involved in the mechanisms that have been described during As vasculotoxicity in mammals. Genes correlated with Cd were involved in cell cycle and energy metabolism. For c-HCH, genes were involved in lipolysis and cell growth. Genes associated with HSI were involved in protein, lipid and iron metabolisms. Our study proposes specific gene signatures of pollutants and their impacts in fish exposed to multi-stress conditions.

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“…The factor analysis for multiple testing proposed by Causeur et al [16] was used. To test the effect of teeth eruption, the analysis was conducted on 82 infants, for whom teeth eruption had occurred between 3 and 6 months (n = 24) or not (n = 58).…”

Section: Effect Of Teeth Eruption and Exposure To Solid Foodsmentioning

confidence: 99%

Human infant saliva peptidome is modified with age and diet transition

Morzel

Jeannin²,

Lucchi³

et al. 2012

Journal of Proteomics

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Factor Analysis for Multiple Testing (FAMT): AnRPackage for Large-Scale Significance Testing under Dependence

Cited by 14 publications

References 17 publications

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels

Human infant saliva peptidome is modified with age and diet transition

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