Pathway-based analysis of microarray and RNAseq data using pathway processor 2.0

Luca Beltrame, Luca Bianco, Paolo Fontana, Duccio Cavalieri

Research output: Contribution to journalArticle

Abstract

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 topologyaware 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.

Original languageEnglish
Article numberbi0706s41
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL.41
DOIs
Publication statusPublished - 2013

Keywords

  • Biological pathways
  • Gene expression analysis
  • Web tool

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

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