PAGE: Parametric Analysis of Gene Set Enrichment
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Corresponding authors: Seon-Young Kim kimsy@kribb.re.kr - David J Volsky djv4@columbia.edu
BMC Bioinformatics 2005, 6:144 doi:10.1186/1471-2105-6-144
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Proceedings
Vitoantonio Bevilacqua, Paolo Pannarale, Mirko Abbrescia, Claudia Cava, Angelo Paradiso, Stefania Tommasi BMC Bioinformatics 2012, 13(Suppl 7):S9 (8 May 2012) |
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Research
QTL/microarray approach using pathway information Hirokazu Matsuda, Yukio Taniguchi, Hiroaki Iwaisaki Algorithms for Molecular Biology 2012, 7:1 (15 January 2012) |
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Proceedings
SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment Jaehoon Lee, Soyeon Ahn, Sohee Oh, Bruce Weir, Taesung Park BMC Systems Biology 2011, 5(Suppl 2):S11 (14 December 2011) |
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Research article
Vivek A Bhadri, Mark J Cowley, Warren Kaplan, Toby N Trahair, Richard B Lock BMC Genomics 2011, 12:565 (17 November 2011) |
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Methodology article
SegMine workflows for semantic microarray data analysis in Orange4WS Vid Podpečan, Nada Lavrač, Igor Mozetič, Petra Novak, Igor Trajkovski, Laura Langohr, Kimmo Kulovesi, Hannu Toivonen, Marko Petek, Helena Motaln, Kristina Gruden BMC Bioinformatics 2011, 12:416 (26 October 2011) |
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Research article
Koji Kadota, Kentaro Shimizu BMC Bioinformatics 2011, 12:227 (6 June 2011) |
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Software
PhenoFam-gene set enrichment analysis through protein structural information Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M Teresa Pisabarro, Frank Buchholz BMC Bioinformatics 2010, 11:254 (17 May 2010) |
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Research article
Hans-Ulrich Klein, Christian Ruckert, Alexander Kohlmann, Lars Bullinger, Christian Thiede, Torsten Haferlach, Martin Dugas BMC Bioinformatics 2009, 10:422 (15 December 2009) |
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Software
Enrico Glaab, Jonathan M Garibaldi, Natalio Krasnogor BMC Bioinformatics 2009, 10:358 (28 October 2009) |
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Research article
Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G Wiebe, Laura Ruohonen, Merja Penttilä BMC Genomics 2009, 10:461 (5 October 2009) |
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Methodology article
Tao Xu, JianLei Gu, Yan Zhou, LinFang Du BMC Bioinformatics 2009, 10:240 (5 August 2009) |
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Research article
GAGE: generally applicable gene set enrichment for pathway analysis Weijun Luo, Michael S Friedman, Kerby Shedden, Kurt D Hankenson, Peter J Woolf BMC Bioinformatics 2009, 10:161 (27 May 2009) |
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Research article
Gene set internal coherence in the context of functional profiling David Montaner, Pablo Minguez, Fátima Al-Shahrour, Joaquín Dopazo BMC Genomics 2009, 10:197 (27 April 2009) |
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Method
Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data. |
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Methodology article
A general modular framework for gene set enrichment analysis Marit Ackermann, Korbinian Strimmer BMC Bioinformatics 2009, 10:47 (3 February 2009) |
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Method
Whole genome transcriptome polymorphisms in Arabidopsis thaliana Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, Justin O Borevitz Genome Biology 2008, 9:R165 (24 November 2008) New methods for detecting global patterns of gene expression and splicing variation in natural Arabidopsis thaliana populations. |
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Methodology article
Gene set analyses for interpreting microarray experiments on prokaryotic organisms Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C Taylor BMC Bioinformatics 2008, 9:469 (5 November 2008) |
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Research article
Chris Cheadle, Maria Nesterova, Tonya Watkins, Kathleen C Barnes, John C Hall, Antony Rosen, Kevin G Becker, Yoon S Cho-Chung BMC Medical Genomics 2008, 1:43 (26 September 2008) Overexpression of the regulatory subunit of cAMP-dependent protein kinase (PKA) in ovarian cancer cells causes hyperproliferation for the RI isoform and differentiation for RII, suggesting that PKA may be pivotal in disease progression.
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Research article
Pål A Olsvik, Kai K Lie, Eva Mykkeltvedt, Ole B Samuelsen, Kjell Petersen, Anne-Kristin Stavrum, Bjørn T Lunestad BMC Pharmacology 2008, 8:16 (11 September 2008) |
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Methodology article
Testing gene set enrichment for subset of genes: Sub-GSE Xiting Yan, Fengzhu Sun BMC Bioinformatics 2008, 9:362 (2 September 2008) |
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Methodology article
Stephen W Tanner, Pankaj Agarwal BMC Bioinformatics 2008, 9:348 (22 August 2008) |
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Research article
Integrative analysis of RUNX1 downstream pathways and target genes Joëlle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, Matthew E Ritchie, Frédéric Schütz, Ping Cannon, Marjorie Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, Terence P Speed, Maria Kavallaris, Gordon K Smyth, Hamish S Scott BMC Genomics 2008, 9:363 (31 July 2008) |
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Methodology article
A gene sets approach for identifying prognostic gene signatures for outcome prediction Seon-Young Kim, Yong Sung Kim BMC Genomics 2008, 9:177 (16 April 2008) |
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Research article
Ana Oliveira, Kiran Patil, Jens Nielsen BMC Systems Biology 2008, 2:17 (8 February 2008) |
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Review
Dissecting complex transcriptional responses using pathway-level scores based on prior information Harmen J Bussemaker, Lucas D Ward, Andre Boorsma BMC Bioinformatics 2007, 8(Suppl 6):S6 (27 September 2007) |
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Methodology article
Computation of significance scores of unweighted Gene Set Enrichment Analyses Andreas Keller, Christina Backes, Hans-Peter Lenhof BMC Bioinformatics 2007, 8:290 (6 August 2007) |
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Research article
Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li BMC Bioinformatics 2007, 8:194 (11 June 2007) |
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Methodology article
Seon-Young Kim, YongSung Kim BMC Bioinformatics 2006, 7:330 (4 July 2006) |
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Research article
Identification of QTLs controlling gene expression networks defined a priori Daniel J Kliebenstein, Marilyn AL West, Hans van Leeuwen, Olivier Loudet, RW Doerge, Dina A St Clair BMC Bioinformatics 2006, 7:308 (16 June 2006) |