Integrative pathway enrichment analysis of multivariate omics data

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S. Fox, Helen Zhu, Diala Abd-Rabbo, Miles W. Mee, Paul C. Boutros and Jüri Reimand ()
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Marta Paczkowska: Ontario Institute for Cancer Research
Jonathan Barenboim: Ontario Institute for Cancer Research
Nardnisa Sintupisut: Ontario Institute for Cancer Research
Natalie S. Fox: Ontario Institute for Cancer Research
Helen Zhu: Ontario Institute for Cancer Research
Diala Abd-Rabbo: Ontario Institute for Cancer Research
Miles W. Mee: Ontario Institute for Cancer Research
Paul C. Boutros: Ontario Institute for Cancer Research
Jüri Reimand: Ontario Institute for Cancer Research

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: Abstract Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

Date: 2020
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DOI: 10.1038/s41467-019-13983-9

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