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首页> 外文期刊>BMC Genomics >Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration
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Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration

机译：Mergeomics：一种Web服务器，用于通过多维数据集成来识别病理路径，网络和关键调节剂

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Background Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. Results To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics.research.idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Conclusions Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators, biological pathways, and gene networks.
机译：背景技术人类疾病通常是分子，细胞和全身水平发生多维变化的结果。基因组技术的最新进展已使捕获这些变化的组学数据集大量涌现。然而，对这些各种数据的单独分析仅提供了零散的理解，并没有捕获疾病机理的整体观点。为了满足对有效整合多种组学数据以获取生物学见解的工具的迫切需求，我们开发了Mergeomics，这是一种计算管道，将多维疾病关联数据与功能基因组学和分子网络相集成，以检索生物学途径，基因网络和中心对疾病发展至关重要的调节剂。结果为了使Mergeomics管道可用于更广泛的研究社区，我们实现了在线，用户友好的Web服务器（http://mergeomics.research.idre.ucla.edu/）。 Web服务器具有Mergeomics管道的模块化实现以及详细的教程。此外，它提供了精选的基因组资源，包括组织特异性表达定量性状基因座，ENCODE功能注释，生物学途径和分子网络，并提供了分析结果的交互式可视化。可以单独使用或灵活组合使用多种计算工具，包括标记依赖过滤（MDF），标记集丰富分析（MSEA），Meta-MSEA和加权密钥驱动器分析（wKDA）。可以上传和实时计算与特定疾病或表型相关的用户定义的摘要级基因组关联数据集（例如遗传，转录组，表观基因组），以产生生物学上可解释的结果，该结果可在线查看并下载以备后用。结论我们的Mergeomics Web服务器为研究人员提供了灵活且用户友好的工具，以组织特定的关键调节剂，生物途径和基因网络的形式，将多维数据集成到疾病机制的整体视图中。

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