UNIT 7.6 Pathway-Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0

  1. Luca Beltrame1,
  2. Luca Bianco2,
  3. Paolo Fontana2,
  4. Duccio Cavalieri2

Published Online: 1 MAR 2013

DOI: 10.1002/0471250953.bi0706s41

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Beltrame, L., Bianco, L., Fontana, P. and Cavalieri, D. 2013. Pathway-Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0. Current Protocols in Bioinformatics. 41:7.6:7.6.1–7.6.12.

Author Information

  1. 1

    Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy

  2. 2

    Research and Innovation Center, Edmund Mach Foundation, San Michele All'Adige, Italy

Publication History

  1. Published Online: 1 MAR 2013


The constant improvement of high-throughput technologies has led to a great increase in generated data per single experiment. Pathway analysis is a widespread method to understand experimental results at the system level. Pathway Processor 2.0 is an upgrade over the original Pathway Processor program developed in 2002, extended to support more species, analysis methods, and RNAseq data in addition to microarrays through a simple Web-based interface. The tool can perform two different types of analysis: the first covers the traditional Fisher's Test used by Pathway Processor and topology-aware analyses, which take into account the propagation of changes over the whole structure of a pathway, and the second is a new pathway-based method to investigate differences between phenotypes of interest. Common problems and troubleshooting are also discussed. Curr. Protoc. Bioinform. 41:7.6.1-7.6.12. © 2013 by John Wiley & Sons, Inc.


  • biological pathways;
  • gene expression analysis;
  • Web tool