Department of Mechanical Engineering, School of Engineering, Cardiff University, Cardiff, UK.
Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain.
Nucleic Acids Res. 2022 Jul 5;50(W1):W551-W559. doi: 10.1093/nar/gkac352.
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/.
PaintOmics 是一个用于使用生物途径图谱对多组学数据集进行综合分析和可视化的网络服务器。PaintOmics 4 有几个显著的更新，可改进和扩展分析。现在支持三个途径数据库：KEGG、Reactome 和 MapMan，为动物和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基于途径的富集方法的空白。代谢物枢纽分析选择在其相邻网络中具有大量显著基因的化合物，表明受基因表达变化的调节。代谢物类活性分析检验了这样一种假设，即代谢物类具有高于预期的显著元素比例，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）对途径的调节作用。我们展示了 PaintOmics 4 在小鼠和植物数据上的性能，以突出这些新的分析功能如何为调节生物学提供新的见解。PaintOmics 4 可在 https://paintomics.org/ 获取。
