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

Beltrame, L.; Bianco, L.; Fontana, P.; Cavalieri, D. (2013). Pathway-based analysis of microarray and RNAseq data using pathway processor 2.0. In: Current protocols in bioinformatics (editor(s) Baxevanis, A.D.). Oxford: Wiley: 7.6.1-7.6.12. ISBN: 9780471250951 doi: 10.1002/0471250953.bi0706s41. handle: http://hdl.handle.net/10449/21933

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

Bianco, Luca;Fontana, Paolo;Cavalieri, Duccio
2013-01-01

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 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
Biological pathways
Gene expression analysis
Web tool
Settore BIO/18 - GENETICA
9780471250951
Beltrame, L.; Bianco, L.; Fontana, P.; Cavalieri, D. (2013). Pathway-based analysis of microarray and RNAseq data using pathway processor 2.0. In: Current protocols in bioinformatics (editor(s) Baxevanis, A.D.). Oxford: Wiley: 7.6.1-7.6.12. ISBN: 9780471250951 doi: 10.1002/0471250953.bi0706s41. handle: http://hdl.handle.net/10449/21933
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