Open Access Highly Accessed Methodology article

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

Andrey Alexeyenko12, Woojoo Lee3, Maria Pernemalm24, Justin Guegan5, Philippe Dessen5, Vladimir Lazar5, Janne Lehtiö24 and Yudi Pawitan6*

Author Affiliations

1 School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden

2 , Science for Life Laboratory, Stockholm, Sweden

3 Department of Statistics, Inha University, Incheon, South Korea

4 Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Stockholm, Sweden

5 Functional Genomics, Institut Gustave Roussy, Villejuif, France

6 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden

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BMC Bioinformatics 2012, 13:226  doi:10.1186/1471-2105-13-226

Published: 11 September 2012

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Additional file 1:

Has three sections. Section A has two figures: In Figure S1, we compared z-scores from GEA to those from MNEA and FNEA. In Figure S2, we compared the NEA scores of individual AGSs versus 264 FGSs for the two omics data. Section B contains the list of pathways used in our lung cancer study. Their meanings and references are also given. For pedagogic purposes, in Section C, we provide a fully worked-out example of analysis of lung cancer data from Bild et al.’s.

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