Pathway‐Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0

Luca Beltrame1, Luca Bianco2, Paolo Fontana2, Duccio Cavalieri2

1 Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy, 2 Research and Innovation Center, Edmund Mach Foundation, San Michele All'Adige, Italy
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.6
DOI:  10.1002/0471250953.bi0706s41
Online Posting Date:  March, 2013
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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.

Keywords: biological pathways; gene expression analysis; Web tool

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Table of Contents

  • Introduction
  • Basic Protocol 1: Functional Analysis of Differentially Expressed Genes
  • Basic Protocol 2: Gene Set Variation Analysis of Microarray or RNAseq Data
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
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