title: Pathway-based analysis of microarray and RNAseq data using Pathway Processor 2.0.
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.
authors.affiliation: Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Beltrame
authors.affiliation: Research and Innovation Center, Edmund Mach Foundation, San Michele All'Adige, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: Research and Innovation Center, Edmund Mach Foundation, San Michele All'Adige, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.affiliation: Research and Innovation Center, Edmund Mach Foundation, San Michele All'Adige, Italy.
authors.forename: Duccio
authors.initials: D
authors.lastname: Cavalieri
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic