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L2L: a simple tool for discovering the hidden significance in microarray expression data
John C Newman, Alan M Weiner
Genome Biol. 2005; 6(9): R81. Published online 2005 August 31. doi: 10.1186/gb-2005-6-9-r81
PMCID:
PMC1242216
Abstract Full Text PDF–1.2M

Is Cited by the Following 42 Articles in this Archive:

Comprehensive literature review and statistical considerations for microarray meta-analysis
George C. Tseng, Debashis Ghosh, Eleanor Feingold
Nucleic Acids Res. 2012 May; 40(9): 3785–3799. Published online 2012 January 19. doi: 10.1093/nar/gkr1265
PMCID:
PMC3351145
Abstract Full Text PDF–3.7M Supplementary Material
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
Alla Karnovsky, Terry Weymouth, Tim Hull, V. Glenn Tarcea, Giovanni Scardoni, Carlo Laudanna, Maureen A. Sartor, Kathleen A. Stringer, H. V. Jagadish, Charles Burant, Brian Athey, Gilbert S. Omenn
Bioinformatics. 2012 February 1; 28(3): 373–380. Published online 2011 November 30. doi: 10.1093/bioinformatics/btr661
PMCID:
PMC3268237
Free in PMC on 2013/02/01
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
Mikhail G Dozmorov, Jonathan D Wren
BMC Bioinformatics. 2011; 12(Suppl 10): S2. Published online 2011 October 18. doi: 10.1186/1471-2105-12-S10-S2
PMCID:
PMC3236842
Abstract Full Text PDF–2.6M
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc
PLoS One. 2011; 6(7): e21800. Published online 2011 July 18. doi: 10.1371/journal.pone.0021800
PMCID:
PMC3138752
Abstract Full Text PDF–1.8M
Gene set analysis for longitudinal gene expression data
Ke Zhang, Haiyan Wang, Arne C Bathke, Solomon W Harrar, Hans-Peter Piepho, Youping Deng
BMC Bioinformatics. 2011; 12: 273. Published online 2011 July 3. doi: 10.1186/1471-2105-12-273
PMCID:
PMC3142525
Abstract Full Text PDF–395K
Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes
Steven X Ge
BMC Syst Biol. 2011; 5: 87. Published online 2011 May 29. doi: 10.1186/1752-0509-5-87
PMCID:
PMC3123203
Abstract Full Text PDF–4.4M Supplementary Material
Radiation Acts on the Microenvironment to Affect Breast Carcinogenesis by Distinct Mechanisms that Decrease Breast Cancer Latency and Affect Tumor Type
David H. Nguyen, Hellen A. Oketch-Rabah, Irineu Illa-Bochaca, Felipe C. Geyer, Jorge S. Reis-Filho, Jian-Hua Mao, Shraddha A. Ravani, Jiri Zavadil, Alexander D. Borowsky, D. Joseph Jerry, Karen A. Dunphy, Jae Hong Seo, Sandra Haslam, Daniel Medina, Mary Helen Barcellos-Hoff
Cancer Cell. Author manuscript; available in PMC 2012 May 17.
Published in final edited form as: Cancer Cell. 2011 May 17; 19(5): 640–651. doi: 10.1016/j.ccr.2011.03.011
PMCID:
PMC3110779
Abstract Full Text PDF–5.2M Supplementary Material
Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties
Pablo Minguez, Joaquin Dopazo
PLoS One. 2011; 6(3): e17474. Published online 2011 March 7. doi: 10.1371/journal.pone.0017474
PMCID:
PMC3049771
Abstract Full Text PDF–625K Supplementary Material
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein, Rémi Houlgatte
BMC Genomics. 2011; 12: 113. Published online 2011 February 16. doi: 10.1186/1471-2164-12-113
PMCID:
PMC3049149
Abstract Full Text PDF–3.5M Supplementary Material
WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results
Vineet K Joshi, Johannes M Freudenberg, Zhen Hu, Mario Medvedovic
Source Code Biol Med. 2011; 6: 3. Published online 2011 January 17. doi: 10.1186/1751-0473-6-3
PMCID:
PMC3033799
Abstract Full Text PDF–1.4M
Specific and Shared Targets of Ephrin A Signaling in Epidermal Keratinocytes
Rebecca Walsh, Miroslav Blumenberg
J Biol Chem. 2011 March 18; 286(11): 9419–9428. Published online 2010 December 30. doi: 10.1074/jbc.M110.197087
PMCID:
PMC3059010
Abstract Full Text Supplementary Material
Toward a complete in silico, multi-layered embryonic stem cell regulatory network
Huilei Xu, Christoph Schaniel, Ihor R. Lemischka, Avi Ma’ayan
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 Nov–Dec; 2(6): 708–733. doi: 10.1002/wsbm.93
PMCID:
PMC2951283
Abstract Full Text PDF–1.9M
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes
Fátima Al-Shahrour, Pablo Minguez, Tomás Marqués-Bonet, Elodie Gazave, Arcadi Navarro, Joaquín Dopazo
PLoS Comput Biol. 2010 October; 6(10): e1000953. Published online 2010 October 7. doi: 10.1371/journal.pcbi.1000953
PMCID:
PMC2951340
Abstract Full Text PDF–671K Supplementary Material
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures
Miguel Vazquez, Ruben Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, Jose M. Carazo, Francisco Tirado, Alberto Pascual-Montano, Pedro Carmona-Saez
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W228–W232. Published online 2010 May 29. doi: 10.1093/nar/gkq476
PMCID:
PMC2896165
Abstract Full Text PDF–1.1M Supplementary Material
Discovering causal signaling pathways through gene-expression patterns
Jignesh R. Parikh, Bertram Klinger, Yu Xia, Jarrod A. Marto, Nils Blüthgen
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W109–W117. Published online 2010 May 21. doi: 10.1093/nar/gkq424
PMCID:
PMC2896193
Abstract Full Text PDF–633K Supplementary Material
Integrative Meta-Analysis of Differential Gene Expression in Acute Myeloid Leukemia
Brady G. Miller, John A. Stamatoyannopoulos
PLoS One. 2010; 5(3): e9466. Published online 2010 March 1. doi: 10.1371/journal.pone.0009466
PMCID:
PMC2830886
Abstract Full Text PDF–1012K Supplementary Material
Genomics Portals: integrative web-platform for mining genomics data
Kaustubh Shinde, Mukta Phatak, Freudenberg M Johannes, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jaroslaw Meller, Mario Medvedovic
BMC Genomics. 2010; 11: 27. Published online 2010 January 13. doi: 10.1186/1471-2164-11-27
PMCID:
PMC2824719
Abstract Full Text PDF–2.3M Supplementary Material
Quantitative comparison of microarray experiments with published leukemia related gene expression signatures
Hans-Ulrich Klein, Christian Ruckert, Alexander Kohlmann, Lars Bullinger, Christian Thiede, Torsten Haferlach, Martin Dugas
BMC Bioinformatics. 2009; 10: 422. Published online 2009 December 15. doi: 10.1186/1471-2105-10-422
PMCID:
PMC2803858
Abstract Full Text PDF–334K Supplementary Material
Web-based interrogation of gene expression signatures using EXALT
Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L George, Jr, Yajun Yi
BMC Bioinformatics. 2009; 10: 420. Published online 2009 December 14. doi: 10.1186/1471-2105-10-420
PMCID:
PMC2799423
Abstract Full Text PDF–1.3M
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery
Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto, Yasushi Okuno
BMC Genomics. 2009; 10: 411. Published online 2009 September 3. doi: 10.1186/1471-2164-10-411
PMCID:
PMC2748096
Abstract Full Text PDF–1016K Supplementary Material
Functional Profiling Reveals Critical Role for miRNA in Differentiation of Human Mesenchymal Stem Cells
Angela Schoolmeesters, Teresa Eklund, Devin Leake, Annaleen Vermeulen, Queta Smith, Shelley Force Aldred, Yuriy Fedorov
PLoS ONE. 2009; 4(5): e5605. Published online 2009 May 19. doi: 10.1371/journal.pone.0005605
PMCID:
PMC2680014
Abstract Full Text PDF–224K Supplementary Material
Cross species analysis of microarray expression data
Yong Lu, Peter Huggins, Ziv Bar-Joseph
Bioinformatics. 2009 June 15; 25(12): 1476–1483. Published online 2009 April 8. doi: 10.1093/bioinformatics/btp247
PMCID:
PMC2732912
Abstract Full Text PDF–489K
Genome-wide impact of Androgen Receptor Trapped Clone-27 Loss on Androgen-regulated Transcription in Prostate Cancer Cells
Jerome C. Nwachukwu, Paolo Mita, Rachel Ruoff, Susan Ha, Qianben Wang, S. Joseph Huang, Samir S. Taneja, Myles Brown, William L. Gerald, Michael J. Garabedian, Susan K. Logan
Cancer Res. Author manuscript; available in PMC 2010 April 1.
Published in final edited form as: Cancer Res. 2009 April 1; 69(7): 3140–3147. Published online 2009 March 24. doi: 10.1158/0008-5472.CAN-08-3738
PMCID:
PMC2702238
Abstract Full Text PDF–1.5M Supplementary Material
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
Da Wei Huang, Brad T. Sherman, Richard A. Lempicki
Nucleic Acids Res. 2009 January; 37(1): 1–13. Published online 2009 January. doi: 10.1093/nar/gkn923
PMCID:
PMC2615629
Abstract Full Text PDF–239K Supplementary Material
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J Butte
BMC Bioinformatics. 2008; 9: 548. Published online 2008 December 18. doi: 10.1186/1471-2105-9-548
PMCID:
PMC2629779
Abstract Full Text PDF–284K Supplementary Material
Gene Expression Signatures Predictive of Early Response and Outcome in High-Risk Childhood Acute Lymphoblastic Leukemia: A Children's Oncology Group Study
Deepa Bhojwani, Huining Kang, Renee X. Menezes, Wenjian Yang, Harland Sather, Naomi P. Moskowitz, Dong-Joon Min, Jeffrey W. Potter, Richard Harvey, Stephen P. Hunger, Nita Seibel, Elizabeth A. Raetz, Rob Pieters, Martin A. Horstmann, Mary V. Relling, Monique L. den Boer, Cheryl L. Willman, William L. Carroll
J Clin Oncol. 2008 September 20; 26(27): 4376–4384. doi: 10.1200/JCO.2007.14.4519
PMCID:
PMC2736991
Abstract Full Text PDF–363K Supplementary Material
SQUAT: A web tool to mine human, murine and avian SAGE data
Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, Jean-François Boulicaut, Jérémy Besson, Ruggero G Pensa, Olivier Gandrillon
BMC Bioinformatics. 2008; 9: 378. Published online 2008 September 18. doi: 10.1186/1471-2105-9-378
PMCID:
PMC2567996
Abstract Full Text PDF–1.3M Supplementary Material
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
Qi Zheng, Xiu-Jie Wang
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W358–W363. Published online 2008 July 1. doi: 10.1093/nar/gkn276
PMCID:
PMC2447756
Abstract Full Text PDF–475K Supplementary Material
Gene expression profiling provides insights into the pathways involved in inflammatory arthritis development: murine model of Lyme disease
Jennifer C. Miller, Ying Ma, Hillary Crandall, Xiaohui Wang, Janis J. Weis
Exp Mol Pathol. Author manuscript; available in PMC 2009 August 1.
Published in final edited form as: Exp Mol Pathol. 2008 August; 85(1): 20–27. Published online 2008 April 8. doi: 10.1016/j.yexmp.2008.03.004
PMCID:
PMC2565650
Abstract Full Text PDF–1.1M
Musashi1 Modulates Mammary Progenitor Cell Expansion through Proliferin-Mediated Activation of the Wnt and Notch Pathways
Xiao-Yang Wang, Yuzhi Yin, Hongyan Yuan, Toshiyuki Sakamaki, Hideyuki Okano, Robert I. Glazer
Mol Cell Biol. 2008 June; 28(11): 3589–3599. Published online 2008 March 24. doi: 10.1128/MCB.00040-08
PMCID:
PMC2423292
Abstract Full Text PDF–942K Supplementary Material
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