The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.
Keywords: biomarker discovery; data integration; gene expression; meta-analysis; omics data; public tools.
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MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data.OMICS. 2014 Jun;18(6):335-43. doi: 10.1089/omi.2014.0061. OMICS. 2014. PMID: 24910945 Free PMC article.
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies.BMC Bioinformatics. 2011 Apr 11;12:92. doi: 10.1186/1471-2105-12-92. BMC Bioinformatics. 2011. PMID: 21481242 Free PMC article.
Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. 2015. PMID: 26269925 Free Books & Documents. Review.
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.BMC Bioinformatics. 2017 Oct 2;18(1):434. doi: 10.1186/s12859-017-1849-8. BMC Bioinformatics. 2017. PMID: 28969605 Free PMC article.
Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures.Cancers Head Neck. 2020 Jan 21;5:2. doi: 10.1186/s41199-020-0047-y. eCollection 2020. Cancers Head Neck. 2020. PMID: 31988797 Free PMC article. Review.