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

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/.

SUBMITTER: Liu T

PROVIDER: S-EPMC9252773 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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

Liu Tianyuan T Salguero Pedro P Petek Marko M Martinez-Mira Carlos C Balzano-Nogueira Leandro L Ramšak Živa Ž McIntyre Lauren L Gruden Kristina K Tarazona Sonia S Conesa Ana A

Nucleic acids research 20220701 W1

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 ...[more]

PMID: 35609982

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Dataset Information

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

Publications

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

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