PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases.
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases.
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DOI：
10.1093/nar/gkac352
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发表时间：
2022-07-05
影响因子：
14.9
通讯作者：
Conesa, Ana
中科院分区：
文献类型：
--
作者：
Liu, Tianyuan;Salguero, Pedro;Petek, Marko;Martinez-Mira, Carlos;Balzano-Nogueira, Leandro;Ramsak, Ziva;McIntyre, Lauren;Gruden, Kristina;Tarazona, Sonia;Conesa, Ana
PaintOmics是一个网络服务器，用于使用生物路径图对多个组学数据集进行综合分析和可视化。PaintOmics 4有几个值得注意的更新，改进和扩展了分析。现在支持三个途径数据库：KEGG、Reactome和MapMan，为动植物提供更全面的途径知识。新的代谢物分析方法填补了传统途径富集法的空白。代谢物中心分析选择在其邻近网络中具有大量重要基因的化合物，这表明通过基因表达变化进行调控。代谢物类别活性分析测试了代谢类别具有高于预期的重要元素比例的假设，表明这些化合物在实验中受到调节。最后，PaintOmics 4包括一个调节组学模块，用于分析跨调节层(microRNA和转录因子、RNA结合蛋白)对调节途径的贡献。我们展示了PaintOmics 4在鼠标和植物数据上的性能，以强调这些新的分析功能如何为调节生物学提供新的见解。PaintOmics 4在https://paintomics.org/.上有售Paintomics 4功能概述。
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/. Overview of Paintomics 4 functionalities.
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影响因子：
--
作者：
Kuo TC;Tian TF;Tseng YJ
通讯作者：
Tseng YJ
影响因子：
9.4
作者：
Lima, Taysla R. A.;Carvalho, Ellen C. D.;Araujo, Francisca S.
通讯作者：
Araujo, Francisca S.
DOI：
10.1093/bioinformatics/btw334
发表时间：
2016-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Garcia-Garcia F;Panadero J;Dopazo J;Montaner D
通讯作者：
Montaner D
影响因子：
20.3
作者：
Ferreiros-Vidal, Isabel;Carroll, Thomas;Merkenschlager, Matthias
通讯作者：
Merkenschlager, Matthias
影响因子：
5.8
作者：
Jensen, Paul A.;Papin, Jason A.
通讯作者：
Papin, Jason A.