@Article{hochreiter:etal:2006,
  author = {Sepp Hochreiter and  Djork-Arne Clevert and Klaus Obermayer},
  title = 	 {A new summarization method for affymetrix probe level data},
  journal = 	 {Bioinformatics},
  year = 	 {2006},
  key = 	 {},
  volume = 	 {22},
  number = 	 {},
  pages = 	 {943-949},
  month = 	 {},
  note =	 {},
  annote = 	 {}
}

@Article{luo:etal:2009,
  author =       {Luo, Weijun and Friedman, Michael and Shedden, Kerby and Hankenson, Kurt and Woolf, Peter},
  title = 	 {{GAGE}: generally applicable gene set enrichment for pathway analysis},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2009},
  volume = 	 {10},
  number = 	 {1},
  pages = 	 {161},
  month = 	 {},
  URL = {http://www.biomedcentral.com/1471-2105/10/161}
}


@Article{luo:etal:2013,
  author =       {Luo, Weijun and Brouwer, Cory},
  title = 	 {{Pathview: an R/Bioconductor package for pathway-based data integration and visualization}},
  journal = 	 {Bioinformatics},
  year = 	 {2013},
  doi =          {10.1093/bioinformatics/btt285},
  volume = 	 {29},
  number = 	 {14},
  pages = 	 {1830-1831},
  month = 	 {},
  URL = {http://bioinformatics.oxfordjournals.org/content/29/14/1830.full}
}

@Article{kim:etal:2005,
  author =       {Kim, SY and Volsky, DJ},
  title = 	 {{PAGE}: parametric analysis of gene set enrichment},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2005},
  key = 	 {},
  volume = 	 {6},
  number = 	 {},
  pages = 	 {144},
  month = 	 {},
  note =	 {},
  annote = 	 {}
}

@Article{subra:etal:2005,
  author =       {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.},
  title = 	 {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles},
  journal = 	 {Proceedings of the National Academy of Sciences of the United States of America},
  year = 	 {2005},
  key = 	 {},
  volume = 	 {102},
  number = 	 {43},
  pages = 	 {15545-15550},
  month = 	 {},
  note =	 {},
  annote = 	 {}
}

@Article{emery:etal:2009,
  author =       {Lyndsey A. Emery and Anusri Tripathi and Chialin King and Maureen Kavanah and Jane Mendez and Michael D. Stone and Antonio de las Morenas and Paola Sebastiani and Carol L. Rosenberg},
  title = 	 {Early Dysregulation of Cell Adhesion and Extracellular Matrix Pathways in Breast Cancer Progression},
  journal = 	 {The American journal of pathology},
  year = 	 {2009},
  key = 	 {},
  volume = 	 {175},
  number = 	 {},
  pages = 	 {1292-1302},
  month = 	 {},
  note =	 {},
  annote = 	 {}
}

@Article{zhang:etal:2009,
author = {Zhang, Jitao David and Wiemann, Stefan}, 
title = {{KEGGgraph: a graph approach to KEGG PATHWAY in R and Bioconductor}},
volume = {25}, 
number = {11}, 
pages = {1470-1471}, 
year = {2009}, 
doi = {}, 
abstract ={Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory.Results: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway.Availability:KEGGgraph is freely available at the Bioconductor web site (http://www.bioconductor.org). KGML files can be downloaded from KEGG FTP site (ftp://ftp.genome.jp/pub/kegg/xml).Contact: j.zhang@dkfz-heidelberg.deSupplementary information: Supplementary data are available at Bioinformatics online.}, 
URL = {}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/25/11/1470.full.pdf+html}, 
journal = {Bioinformatics} 
}