PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

Liu, Tianyuan ORCID: https://orcid.org/0000-0002-8561-6239, Salguero, Pedro, Petek, Marko, Martinez-Mira, Carlos, Balzano-Nogueira, Leandro, Ramsak, Ziva, McIntyre, Lauren, Gruden, Kristina, Tarazona, Sonia and Conesa, Ana 2022. PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. Nucleic Acids Research 50 (W1) , W551–W559. 10.1093/nar/gkac352

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Abstract

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/.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Engineering
Publisher:	Oxford University Press
ISSN:	0305-1048
Date of Acceptance:	25 April 2022
Last Modified:	02 Nov 2022 09:45
URI:	https://orca.cardiff.ac.uk/id/eprint/153898

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