Integrative pathway enrichment analysis of multivariate omics data

Research output: Contribution to journalJournal articleResearchpeer-review


  • Marta Paczkowska
  • Jonathan Barenboim
  • Nardnisa Sintupisut
  • Natalie S. Fox
  • Helen Zhu
  • Diala Abd-Rabbo
  • Miles W. Mee
  • Paul C. Boutros
  • Federico Abascal
  • Samirkumar B. Amin
  • Gary D. Bader
  • Rameen Beroukhim
  • Johanna Bertl
  • Keith A. Boroevich
  • Peter J. Campbell
  • Joana Carlevaro-Fita
  • Dimple Chakravarty
  • Calvin Wing Yiu Chan
  • Ken Chen
  • Jung Kyoon Choi
  • Jordi Deu-Pons
  • Priyanka Dhingra
  • Klev Diamanti
  • Lars Feuerbach
  • J. Lynn Fink
  • Nuno A. Fonseca
  • Joan Frigola
  • Carlo Gambacorti-Passerini
  • Dale W. Garsed
  • Mark Gerstein
  • Gad Getz
  • Abel Gonzalez-Perez
  • Qianyun Guo
  • Ivo G. Gut
  • David Haan
  • Mark P. Hamilton
  • Nicholas J. Haradhvala
  • Arif O. Harmanci
  • Mohamed Helmy
  • Carl Herrmann
  • Julian M. Hess
  • Asger Hobolth
  • Ermin Hodzic
  • Chen Hong
  • Henrik Hornshøj
  • Morten Muhlig Nielsen
  • Jakob Skou Pedersen
  • Nikos Sidiropoulos

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.

Original languageEnglish
Article number735
JournalNature Communications
Issue number1
Publication statusPublished - 5 Feb 2020

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