PaintOmics 4Liu, Tianyuan (Avtor) Salguero, Pedro (Avtor) Petek, Marko (Avtor) Martinez-Mira, Carlos (Avtor) Balzano-Nogueira, Leandro (Avtor) Ramšak, Živa (Avtor) McIntyre, Lauren (Avtor) Gruden, Kristina (Avtor) Tarazona, Sonia (Avtor) Conesa, Ana (Avtor) PaintOmics 4web toolsdatasetsanalysis methodsmolecular biologyPaintOmics 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. 20222024-07-16 03:43:36Neznano19337sl