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Haw R, Loney F, Ong E, et al. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165-179doi: 10.1007/978-1-4939-9873-9_13.
Haw, R., Loney, F., Ong, E., He, Y., & Wu, G. (2020). Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods in molecular biology (Clifton, N.J.), 2074165-179. https://doi.org/10.1007/978-1-4939-9873-9_13
Haw, Robin, et al. "Perform Pathway Enrichment Analysis Using ReactomeFIViz." Methods in molecular biology (Clifton, N.J.) vol. 2074 (2020): 165-179. doi: https://doi.org/10.1007/978-1-4939-9873-9_13
Haw R, Loney F, Ong E, He Y, Wu G. Perform Pathway Enrichment Analysis Using ReactomeFIViz. Methods Mol Biol. 2020;2074:165-179. doi: 10.1007/978-1-4939-9873-9_13. PMID: 31583638.
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Methods Mol Biol. 2020;2074:165-179. doi: 10.1007/978-1-4939-9873-9_13.

Perform Pathway Enrichment Analysis Using ReactomeFIViz.

Methods in molecular biology (Clifton, N.J.)

Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu

Affiliations

  1. Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
  2. Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
  3. University of Michigan Medical School, Ann Arbor, MI, USA.
  4. Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA. [email protected].

PMID: 31583638 DOI: 10.1007/978-1-4939-9873-9_13

Abstract

Modern large-scale biological data analysis often generates a set of significant genes, frequently associated with scores. Pathway-based approaches are routinely performed to understand the functional contexts of these genes. Reactome is the most comprehensive open-access biological pathway knowledge base, widely used in the research community, providing a solid foundation for pathway-based data analysis. ReactomeFIViz is a Cytoscape app built upon Reactome pathways to help users perform pathway- and network-based data analysis and visualization. In this chapter we describe procedures on how to perform pathway enrichment analysis using ReactomeFIViz for a gene score file. We describe two types of analysis: pathway enrichment based on a set of significant genes and GSEA analysis using gene scores without cutoff. We also describe a feature to overlay gene scores onto pathway diagrams, enabling users to understand the underlying mechanisms for up- or down- regulated pathways collected from pathway analysis.

Keywords: Biological pathway; Cytoscape; GSEA; Gene score; Pathway enrichment analysis; Reactome; ReactomeFIViz

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