An experimental evaluation of a loop versus a reference design for two-channel microarrays

Vinciotti, Veronica; Khanin, Raya; D’Alimonte, Davide; Liu, X.; Cattini, N.; Hotchkiss, Graham; Bucca, Giselda; Jesús, Orlando De; Rasaiyaah, Jane; Smith, C. P.; Kellam, Paul; Wit, Ernst

doi:10.1093/bioinformatics/bti022

Cited by 85 publications

(66 citation statements)

References 12 publications

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“…Nevertheless, as there is some evidence for short-lived induction (57), the mosquitoes are held for 24 h postexposure so that any genes that are differentially expressed between groups most likely reflect constitutive rather than induced changes. An interwoven loop design, using three RNA pools from field-collected material and each colony control, was selected for between group comparisons because this experimental design is both more efficient and provides greater power compared with the standard experimental design (58). The experimental design is shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

Identification and validation of a gene causing cross-resistance between insecticide classes inAnopheles gambiaefrom Ghana

Mitchell

Stevenson

Müller

et al. 2012

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

228

255

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In the last decade there have been marked reductions in malaria incidence in sub-Saharan Africa. Sustaining these reductions will rely upon insecticides to control the mosquito malaria vectors. We report that in the primary African malaria vector, Anopheles gambiae sensu stricto, a single enzyme, CYP6M2, confers resistance to two classes of insecticide. This is unique evidence in a disease vector of cross-resistance associated with a single metabolic gene that simultaneously reduces the efficacy of two of the four classes of insecticide routinely used for malaria control. The gene-expression profile of a highly DDT-resistant population of A. gambiae s.s. from Ghana was characterized using a unique whole-genome microarray. A number of genes were significantly overexpressed compared with two susceptible West African colonies, including genes from metabolic families previously linked to insecticide resistance. One of the most significantly overexpressed probe groups (false-discovery rate-adjusted P < 0.0001) belonged to the cytochrome P450 gene CYP6M2. This gene is associated with pyrethroid resistance in wild A. gambiae s.s. populations) and can metabolize both type I and type II pyrethroids in recombinant protein assays. Using in vitro assays we show that recombinant CYP6M2 is also capable of metabolizing the organochlorine insecticide DDT in the presence of solubilizing factor sodium cholate.

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Section: Methodsmentioning

confidence: 99%

Identification and validation of a gene causing cross-resistance between insecticide classes inAnopheles gambiaefrom Ghana

Mitchell

Stevenson

Müller

et al. 2012

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

228

255

View full text Add to dashboard Cite

show abstract

“…Although the inferred expression levels are of arbitrary unit scale, this scaling has the intuitive appeal that all gene expression level measurements are positive, as they should be. Circuit designs of microarray comparisons have been strongly endorsed by statisticians (Kerr and Churchill, 2001;Yang and Speed, 2002) and have demonstrated dramatically improved resolution with regard to identifying differential gene regulation below the twofold level (Townsend and Hartl, 2002;Vinciotti et al, 2005).…”

Section: B Experimental Design For Microarray Experimentsmentioning

confidence: 99%

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

Dunlap

Borkovich

Henn

et al. 2007

Advances in Genetics

198

194

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A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250

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“…Only samples that yielded both high quality and a sufficient quantity of RNA were used. Instead of using a universal reference experimental design, we employed a loop experimental design (for details about this experimental design see references 17,18 ).…”

Section: Sample Preparation and Experimental Designmentioning

confidence: 99%

Using gene expression to predict the secretome of differentiating human preadipocytes

et al. 2009

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Objective: To characterize the secretome of differentiating human preadipocytes using global gene expression profiling. Design: Gene expression was measured using microarrays at days 0, 1, 3, 5, 7 and 10 in primary preadipocytes undergoing adipogenesis (n ¼ 6 independent subjects). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins. Measurements: Gene expression was assessed using microarrays and real-time reverse transcriptase PCR, bioinformatic predictive algorithms were used to identify the secretome of differentiating preadipocytes, and the secretion of the most significant candidates were confirmed at the protein level using western blots or ELISA tests. Gene expression was also assayed in the adipocyte and stroma vascular fraction (SVF) of obese subjects. Results: Microarray analysis identified 33 genes whose expression significantly changed (false discovery rate of 1%) during adipogenesis and code for secreted proteins. Of these genes, 18 are novel candidate adipose tissue 'secretome' genes. Their relative gene expression in adipocyte and SVF of obese subjects revealed that most of these genes are more highly expressed in the SVF. A novel candidate, matrix gla protein (MGP), was upregulated (B30-fold) during adipogenesis, second only to leptin (B50-fold). MGP and another secretome candidate protein, inhibin beta B (INHBB), were detected in the secretion media of adipocytes isolated from adipose tissue explants. Conclusions: Gene expression coupled with predictive bioinformatic algorithms has proved a valid and alternative approach to further define the adipocyte secretome. Many of the novel candidate secretome genes are components of the coagulation and fibrinolytic systems. MGP and INHBB represent new adipokines whose function in adipose tissue remains to be unravelled.

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An experimental evaluation of a loop versus a reference design for two-channel microarrays

Abstract: veronica.vinciotti@brunel.ac.uk.

Cited by 85 publications

References 12 publications

Identification and validation of a gene causing cross-resistance between insecticide classes inAnopheles gambiaefrom Ghana

Identification and validation of a gene causing cross-resistance between insecticide classes inAnopheles gambiaefrom Ghana

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

Using gene expression to predict the secretome of differentiating human preadipocytes

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