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Comprehensive literature review and statistical considerations for microarray meta-analysis.

ABSTRACT: With the rapid advances of various high-throughput technologies, generation of '-omics' data is commonplace in almost every biomedical field. Effective data management and analytical approaches are essential to fully decipher the biological knowledge contained in the tremendous amount of experimental data. Meta-analysis, a set of statistical tools for combining multiple studies of a related hypothesis, has become popular in genomic research. Here, we perform a systematic search from PubMed and manual collection to obtain 620 genomic meta-analysis papers, of which 333 microarray meta-analysis papers are summarized as the basis of this paper and the other 249 GWAS meta-analysis papers are discussed in the next companion paper. The review in the present paper focuses on various biological purposes of microarray meta-analysis, databases and software and related statistical procedures. Statistical considerations of such an analysis are further scrutinized and illustrated by a case study. Finally, several open questions are listed and discussed.

SUBMITTER: Tseng GC

PROVIDER: S-EPMC3351145 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature

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Comprehensive literature review and statistical considerations for microarray meta-analysis.

Tseng George C GC Ghosh Debashis D Feingold Eleanor E

Nucleic acids research 20120119 9

With the rapid advances of various high-throughput technologies, generation of '-omics' data is commonplace in almost every biomedical field. Effective data management and analytical approaches are essential to fully decipher the biological knowledge contained in the tremendous amount of experimental data. Meta-analysis, a set of statistical tools for combining multiple studies of a related hypothesis, has become popular in genomic research. Here, we perform a systematic search from PubMed and m ...[more]

PMID: 22262733

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Project description:PURPOSE:There is a lack of agreement regarding the types of lesions and clinical conditions that should be included in the term "geographic atrophy." Varied and conflicting views prevail throughout the literature and are currently used by retinal experts and other health care professionals. METHODS:We reviewed the nominal definition of the term "geographic atrophy" and conducted a search of the ophthalmologic literature focusing on preceding terminologies and the first citations of the term "geographic atrophy" secondary to age-related macular degeneration. RESULTS:According to the nominal definition, the term "geography" stands for a detailed description of the surface features of a specific region, indicating its relative position. However, it does not necessarily imply that the borders of the region must be sharply demarcated or related to any anatomical structures. The term "geographical areas of atrophy" was initially cited in the 1960s in the ophthalmologic literature in the context of uveitic eye disease and shortly thereafter also for the description of variants of "senile macular degeneration." However, no direct explanation could be found in the literature as to why the terms "geographical" and "geographic" were chosen. Presumably the terms were used as the atrophic regions resembled the map of a continent or well-defined country borders on thematic geographical maps. With the evolution of the terminology, the commonly used adjunct "of the retinal pigment epithelium" was frequently omitted and solely the term "geographic atrophy" prevailed for the nonexudative late-stage of age-related macular degeneration itself. Along with the quantification of atrophic areas, based on different imaging modalities and the use of both manual and semiautomated approaches, various and inconsistent definitions for the minimal lesion diameter or size of atrophic lesions have also emerged. CONCLUSION:Reconsideration of the application of the term "geographic atrophy" in the context of age-related macular degeneration seems to be prudent given ongoing advances in multimodal retinal imaging technology with identification of various phenotypic characteristics, and the observation of atrophy development in eyes under antiangiogenic therapy.

Project description:Background: Brucellosis, a zoonotic disease, infects various hosts, including swine and humans. It has reemerged in recent years as a public health concern, and current studies on brucellosis infection in swine have been conducted worldwide. However, no meta-analyses of global brucellosis infection in swine have been published. The aim of this study was to provide an overview of Brucella species (spp.) in swine worldwide and the factors associated with its persistence. Results: We searched seven databases for published epidemiological studies on brucellosis in pigs, including the Chinese National Knowledge Infrastructure, Wanfang Data, SpringerLink, ScienceDirect, Web of Science, the VIP Chinese Journal Database and PubMed. We selected 119 articles published from January 1, 2000 to January 3, 2020 for inclusion in the meta-analysis and analyzed the data using a random-effects model. Funnel plots and Egger's test showed significant publication bias in the included studies. The results of the sensitivity analysis showed that our study was relatively stable and reliable. The prevalence of brucellosis in swine was 2.1% (95% CI: 1.6-2.6), of which the highest infection rate, which was found in Europe, was 17.4% (95% CI: 11.1-24.9). The prevalence in feral pigs (15.0%, 95% CI: 8.4-23.2) was higher than that in domestic pigs (1.1%, 95% CI 0.2-2.5). The prevalence in high-income countries (15.7%, 95% CI 8.0-25.3) was significantly higher than that in middle- (0.8%, 95% CI 0.5-1.1), and low-income countries (0.1%, 95% CI 0.0-0.2). The prevalence was highest in finishing pigs at 4.9% (95% CI 0.9-11.0), and lowest among suckling pigs at 0% (95% CI 0.0-0.5). Conclusion: The Brucella prevalence in pig herds currently is distributed widely throughout the world. In some countries, swine brucellosis may be a neglected zoonotic disease. We recommend long-term monitoring of the prevalence of brucellosis in domestic and wild pig herds. Attention should also be paid to animal welfare on intensive pig farms; controlling the breeding density may play an important role in reducing the spread of brucellosis among pigs.

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Comprehensive literature review and statistical considerations for microarray meta-analysis.

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Comprehensive literature review and statistical considerations for microarray meta-analysis.

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