Dataset Information

Global meta-analysis of transcriptomics studies.

ABSTRACT: Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy), based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF) model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons.

SUBMITTER: Caldas J

PROVIDER: S-EPMC3935861 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Global meta-analysis of transcriptomics studies.

Caldas José J Vinga Susana S

PloS one 20140226 2

Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy), based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields mu ...[more]

PMID: 24586684

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Project description:BackgroundAlthough protocol registration of systematic reviews/meta-analysis (SR/MA) is still not mandatory, it is highly recommended that authors publish their SR/MA protocols prior to submitting their manuscripts for publication as recommended by the Cochrane guidelines for conducting SR/MAs. our aim was to assess the awareness, obstacles, and opinions of SR/MA authors about the protocol registration process.MethodsA cross-sectional survey study included the authors who published SR/MAs during the period from 2010 to 2016, and they were contacted for participation in our survey study. They were identified through the literature search of SR/MAs in Scopus database. An online questionnaire was sent to each participant via e-mail after receiving their approval to join the study. We have sent 6650 emails and received 275 responses.ResultsA total of 270 authors responses were complete and included in the final analysis. Our results has shown that PROSPERO was the most common database used for protocol registration (71.3%). The registration-to-acceptance time interval in PROSPERO was less than 1 month (99.1%). Almost half of the authors (44.2%) did not register their protocols prior to publishing their SR/MAs and according to their opinion that the other authors lack knowledge of protocol importance and mandance to be registered, was the most commonly reported reason (44.9%). A significant percenatge of respondents (37.4%) believed that people would steal their ideas from protocol databases, while only 5.3% reported that their SR/MA had been stolen. However, the majority (72.9%) of participants have agreed that protocol registries play a role in preventing unnecessary duplication of reviews. Finally, 37.4% of participants agree that SR/MA protocol registration should be mandatory.ConclusionAbout half of the participants believes that the main reason for not registering protocols, is that the other authors lack knowledge concerning obligation and importance to register the SR/MA protocols in advance. Therefore, tools should be available to mandate protocol registration of any SRs beforehand and increasing awareness about the benefits of protocol registration among researchers.

Project description:BackgroundImproved access to effective antiretroviral therapy has meant that people living with HIV (PLHIV) are surviving to older ages. However, PLHIV may be ageing differently to HIV-negative individuals, with dissimilar burdens of non-communicable diseases, such as hypertension. While some observational studies have reported a higher risk of prevalent hypertension among PLHIV compared to HIV-negative individuals, others have found a reduced burden. To clarify the relationship between HIV and hypertension, we identified observational studies and pooled their results to assess whether there is a difference in hypertension risk by HIV status.MethodsWe performed a global systematic review and meta-analysis of published cross-sectional studies that examined hypertension risk by HIV status among adults aged > 15 (PROSPERO: CRD42019151359). We searched MEDLINE, EMBASE, Global Health and Cochrane CENTRAL to August 23, 2020, and checked reference lists of included articles. Our main outcome was the risk ratio for prevalent hypertension in PLHIV compared to HIV-negative individuals. Summary estimates were pooled with a random effects model and meta-regression explored whether any difference was associated with study-level factors.ResultsOf 21,527 identified studies, 59 were eligible (11,101,581 participants). Crude global hypertension risk was lower among PLHIV than HIV-negative individuals (risk ratio 0.90, 95% CI 0.85-0.96), although heterogeneity between studies was high (I2 = 97%, p < 0.0001). The relationship varied by continent, with risk higher among PLHIV in North America (1.12, 1.02-1.23) and lower among PLHIV in Africa (0.75, 0.68-0.83) and Asia (0.77, 0.63-0.95). Meta-regression revealed strong evidence of a difference in risk ratios when comparing North American and European studies to African ones (North America 1.45, 1.21-1.74; Europe 1.20, 1.03-1.40).ConclusionsOur findings suggest that the relationship between HIV status and prevalent hypertension differs by region. The results highlight the need to tailor hypertension prevention and care to local contexts and underscore the importance of rapidly optimising integration of services for HIV and hypertension in the worst affected regions. The role of different risk factors for hypertension in driving context-specific trends remains unclear, so development of further cohorts of PLHIV and HIV-negative controls focused on this would also be valuable.

Dataset Information

Global meta-analysis of transcriptomics studies.

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Global meta-analysis of transcriptomics studies.

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