Document Detail


Pathway-Based Analysis of Microarray and RNAseq Data Using Pathway Processor 2.0.
MedLine Citation:
PMID:  23504935     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
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.
Authors:
Luca Beltrame; Luca Bianco; Paolo Fontana; Duccio Cavalieri
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]     Volume:  Chapter 7     ISSN:  1934-340X     ISO Abbreviation:  Curr Protoc Bioinformatics     Publication Date:  2013 Mar 
Date Detail:
Created Date:  2013-03-18     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101157830     Medline TA:  Curr Protoc Bioinformatics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  Unit7.6     Citation Subset:  IM    
Affiliation:
Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy.
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