20.500.12556/DiRROS-19337 PaintOmics 4 new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases 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 web tools datasets analysis methods molecular biology true false true Angleški jezik Ni določen Neznano 2024-07-16 03:43:36 2024-07-17 09:01:14 2026-01-27 07:12:51 0000-00-00 00:00:00 2022 0 0 Ostali avtorji: Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa; Članek v PDF formatu obsega 9 str.; First online: 24 May 2022; str. W551-W559 iss. W1 Vol. 50 2022 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2022-05-24 577 0305-1048 10.1093/nar/gkac352 110574851 https://doi.org/10.1093/nar/gkac352 1 d1d1a474-4314-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=26661 RAZ_Liu_Tianyuan_2022.pdf RAZ_Liu_Tianyuan_2022.pdf 1 3B6A31A08FF7A627A2447A7E593E8DE1 8845d4127f87e170f1971512f06b8d3d13191557ab7f0459569b41d04607f84c 61902a6a-43fa-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=26809 Nacionalni inštitut za biologijo 0 0 0