Analysis of whole-genome microarray replicates using mixed models

Wernisch, Lorenz; Kendall, Sharon L.; Soneji, Shamit; Wietzorrek, Andreas; Parish, Tanya; Hinds, Jason; Butcher, Philip D.; Stoker, Neil G.

doi:10.1093/bioinformatics/19.1.53

Cited by 75 publications

(60 citation statements)

References 17 publications

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“…We have previously seen that deletion of a 2CR can have an indirect effect on gene expression. With TrcS the cells appeared to be stressed and several genes were differentially expressed in response to the stress rather than as a direct result of the regulator deletion (Wernisch et al, 2003). The data for this strain look as if a similar stress response is occurring.…”

Section: Down-regulated Genesmentioning

confidence: 87%

The senX3–regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence

et al. 2003

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Two-component regulatory systems have been widely implicated in bacterial virulence. To investigate the role of one such system in Mycobacterium tuberculosis, a strain was constructed in which the senX3-regX3 system was deleted by homologous recombination. The mutant strain (Tame15) showed a growth defect after infection of macrophages and was attenuated in both immunodeficient and immunocompetent mice. Competitive hybridization of total RNA from the wild-type and mutant strains to a whole-genome microarray was used to identify changes in gene expression resulting from the deletion. One operon was highly up-regulated in the mutant, indicating that regX3 probably has a role as a repressor of this operon. Other genes which were up-or down-regulated were also identified. Many of the genes showing down-regulation are involved in normal growth of the bacterium, indicating that the mutant strain is subject to some type of growth slow-down or stress. Genes showing differential expression were further grouped according to their pattern of gene expression under other stress conditions. From this analysis 50 genes were identified which are the most likely to be controlled by RegX3. Most of these genes are of unknown function and no obvious motifs were found upstream of the genes identified. Thus, it has been demonstrated that the senX3-regX3 two-component system is involved in the virulence of M. tuberculosis and a number of genes controlled by this system have been identified.

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Section: Down-regulated Genesmentioning

confidence: 87%

The senX3–regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence

et al. 2003

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“…81 This could stem from dysregulation of the trcRS operon, reported to include the mmpS5/mmpL5 (Rv0677/Rv0676) transporter and a bacteroferritin, bfrB (Rv3841). 82 Other deletions. Deletions affecting other genes with a potential impact on virulence have also been found in certain BCG strains.…”

Section: Attenuation Of Bcg After 1924mentioning

confidence: 99%

BCG Vaccines: Their mechanisms of attenuation and impact on safety and protective efficacy

Liu

Tran²,

Leung³

et al. 2009

Human Vaccines

125

117

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by MDR strains that are also resistant to a fluoroquinolone and at least one second-line injectable agent (amikacin, kanamycin and/or capreomycin), caught the world's attention after an outbreak in KwaZulu-Natal, South Africa, where 52 of 53 infected patients died. 2 HIV co-infection was a contributing factor in most of these deaths, and indeed, a deadly association between HIV and TB has been known almost since the start of the HIV-epidemic. Of the 1.7 million people who died from TB in 2006, an estimated 200,000 were co-infected with HIV. 1 Because of these situations, effective approaches alternative to antibiotics are urgently needed for the control of TB.Bacille Calmette-Guérin (BCG), an attenuated strain of Mycobacterium bovis (M. bovis), is currently the only available vaccine against TB. Since 1974, BCG vaccination has been included in the WHO Expanded Program on Immunization. 3 It is estimated that more than 3 billion individuals have been immunized with BCG and over 100 million doses of BCG are administered annually, making it the most widely used vaccine in humans. 3 Meta-analysis studies have confirmed that BCG protects children, providing >80% efficacy against severe forms of TB, including tuberculous meningitis and miliary TB. 4,5 In contrast, evidence for protection against pulmonary TB in adolescents and adults remains contentious as efficacy estimates from clinical trials, observational case control studies and contact studies range from 0 to 80%. 6,7 The reasons for the variable protective efficacy are unknown but several hypotheses have been proposed, including differences among the vaccine strains used in clinical studies, exposure of trial populations to environmental mycobacteria, nutritional or genetic differences in human populations, differences in trial methods, and variations among clinical M. tb strains. 8-13 These explanations are not mutually exclusive and all may contribute to the heterogeneity in vaccine efficacy.A key aspect of this issue may concern the nature of BCG attenuation. Although it is generally considered safe and has been used as a human vaccine since the 1920s, the mechanisms of BCG attenuation remain largely unknown. This is further complicated by the fact that BCG is not a single strain, but instead comprises a number of substrains that exhibit phenotypic and biochemical differences. 14 BCG strains also exhibit differences in residual virulence level. [15][16][17] However, side effects were often attributed to variations in the viability of vaccines during preparation procedures (e.g., freezedrying). 14 In other words, the observed differential virulence among Mycobacterium bovis Bacille Calmette-Guérin (BCG) was developed as an attenuated live vaccine for tuberculosis control nearly a century ago. Despite being the most widely used vaccine in human history, the mechanisms of attenuation of BCG remain poorly understood. BCG is not a single organism, but comprises a number of substrains that differ in genotypes and phenotypes. The impacts of these differences on BCG...

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“…However, methods for detecting the genuine changes in the gene expression levels in cells or tissues are still evolving. [1][2][3][4][5][6][7][8][9][10][11] A straightforward method for comparing two expression levels of genes is the traditional two-sample t-test. The basic problem with the t-test in microarray experiments, however, is that the repetition is restricted within a small number in most cases, because experiments are costly or tedious to repeat.…”

mentioning

confidence: 99%

Test of Significant Differences with a priori Probability in Microarray Experiments

et al. 2003

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The advent of high-throughput array technology has now made it possible to collect data on thousands to tens of thousands of genes simultaneously. However, methods for detecting the genuine changes in the gene expression levels in cells or tissues are still evolving. [1][2][3][4][5][6][7][8][9][10][11] A straightforward method for comparing two expression levels of genes is the traditional two-sample t-test. The basic problem with the t-test in microarray experiments, however, is that the repetition is restricted within a small number in most cases, because experiments are costly or tedious to repeat. Although the importance in replication has been illustrated, 1,3,6,9 situations often arise where only single or duplicate experiments for each condition are allowed.The purpose of this paper is to put forward a method for testing the significant differences of the gene expression levels under a single pair of experiments (a control experiment and treatment experiment). In order to take into account the stochastic aspects of gene expressions, we model our algorithm on the t-test. In our approach and the t-test, the SD estimates of the gene expression levels are a criterion for the statistical judgment, but one of the key differences is how to estimate the SD for each gene.In the t-test, the SD estimates are derived from the same data set as those to be judged by the t-test, itself. This fact can be closely connected with the above-mentioned problem of replication. In our approach, the SD estimates, referred to here as a priori SD, are obtained from experimental results which are different from the target data set of the judgment.Statistics tells that the variability in the estimates of SD obeys the chi-squares distribution and is much larger than the variability in the estimates of averages, as long as the estimates are obtained by repetition. That is, the estimates of averages are more reliable. The t-test uses the SD estimates directly, but in this paper, the a prior SD is given as a function of the average of the gene expression levels. Then, we can easily expect that our approach can provide more stable judgment, but needs a sound model for the a prior SD.The idea of the a priori SD is not novel in the area of analytical chemistry. Since more than three decades ago, there have been published many theories and methods for estimating SD with no recourse to repetition, especially in instrumental analyses. [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] In spite of varied symbols and terminology in the literature, the largest part of uncertainty equations proposed can take a universal form:where RSD denotes the relative standard deviation of measurements, sB denotes blank SD, A measurements (e.g., area), and I independent error. To our knowledge, Huber et al. A traditional method for comparing two expression levels of genes in microarray experiments is the two-sample t-test. Because of the difficulty in using a large number of microarrays, an alternative method is required which can provide a relia...

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Analysis of whole-genome microarray replicates using mixed models

Abstract: All methods and data discussed are available in the package YASMAhttp://www.cryst.bbk.ac.uk/wernisch/yasma.html for the statistical data analysis system R (http://www.R-project.org).

Cited by 75 publications

References 17 publications

The senX3–regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence

The senX3–regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence

BCG Vaccines: Their mechanisms of attenuation and impact on safety and protective efficacy

Test of Significant Differences with a priori Probability in Microarray Experiments

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