3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
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DOI：
10.1186/1752-0509-7-64
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发表时间：
2013-07-23
影响因子：
--
通讯作者：
Tseng YJ
中科院分区：
文献类型：
--
作者：
Kuo TC;Tian TF;Tseng YJ
多个转录组学，蛋白质组学和代谢组学数据集的综合和比较分析需要对工具和背景概念有深入的了解。因此，用户进行此类分析具有挑战性，突出表明需要为此目的使用单一工具。3 Omics一键式网络工具的开发旨在通过结合五种常用分析来可视化和快速整合多个人类转录组间或转录组内、蛋白质组和代谢组数据：相关网络、共表达、表型分析、途径富集和GO（基因本体论）富集。3 Omics生成组间相关网络，以可视化所有转录物、蛋白质和代谢物的数据与时间或实验条件的关系。如果只输入了三个组学数据集中的两个，那么3 Omics会通过对PubMed数据库进行文本挖掘来补充与输入数据相关的缺失转录本、蛋白质或代谢物信息。3 Omics的共表达分析有助于揭示不同组学数据集之间共享的功能。3 Omics的表型分析将在线孟德尔遗传与可用的转录本或蛋白质数据整合在一起。3 Omics对代谢组学数据的途径富集分析揭示了KEGG/HumanCyc数据库中富集的途径。3 Omics执行基于基因本体的统计功能富集分析，以显示转录组实验中显著过度代表的GO术语。虽然3 Omics的主要应用是集成多个组学数据集，但它也能够分析单个组学数据集。从案例研究1和2中的3 Omics分析中获得的信息也与文献中的综合结果一致。3 Omics将现有软件的优势和功能整合到一个平台中，从而简化了数据分析，并使用户能够进行一键集成分析。可视化和分析结果可供下载，以供用户进一步定制和分析。3 Omics软件可以在http://3omics.cmdm.tw上免费访问。
Integrative and comparative analyses of multiple transcriptomics, proteomics and metabolomics datasets require an intensive knowledge of tools and background concepts. Thus, it is challenging for users to perform such analyses, highlighting the need for a single tool for such purposes. The 3Omics one-click web tool was developed to visualize and rapidly integrate multiple human inter- or intra-transcriptomic, proteomic, and metabolomic data by combining five commonly used analyses: correlation networking, coexpression, phenotyping, pathway enrichment, and GO (Gene Ontology) enrichment. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for all transcripts, proteins and metabolites. If only two of three omics datasets are input, then 3Omics supplements the missing transcript, protein or metabolite information related to the input data by text-mining the PubMed database. 3Omics’ coexpression analysis assists in revealing functions shared among different omics datasets. 3Omics’ phenotype analysis integrates Online Mendelian Inheritance in Man with available transcript or protein data. Pathway enrichment analysis on metabolomics data by 3Omics reveals enriched pathways in the KEGG/HumanCyc database. 3Omics performs statistical Gene Ontology-based functional enrichment analyses to display significantly overrepresented GO terms in transcriptomic experiments. Although the principal application of 3Omics is the integration of multiple omics datasets, it is also capable of analyzing individual omics datasets. The information obtained from the analyses of 3Omics in Case Studies 1 and 2 are also in accordance with comprehensive findings in the literature. 3Omics incorporates the advantages and functionality of existing software into a single platform, thereby simplifying data analysis and enabling the user to perform a one-click integrated analysis. Visualization and analysis results are downloadable for further user customization and analysis. The 3Omics software can be freely accessed at http://3omics.cmdm.tw.
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