Inferring transcriptional modules from ChIP-chip, motif and microarray data
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* Corresponding author: Kathleen Marchal kathleen.marchal@biw.kuleuven.be
Genome Biology 2006, 7:R37 doi:10.1186/gb-2006-7-5-r37
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An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules Huaxia Qin, Michael WY Chan, Sandya Liyanarachchi, Curtis Balch, Dustin Potter, Irene J Souriraj, Alfred SL Cheng, Francisco J Agosto-Perez, Elena V Nikonova, Pearlly S Yan, Huey-Jen Lin, Kenneth P Nephew, Joel H Saltz, Louise C Showe, Tim HM Huang, Ramana V Davuluri BMC Systems Biology 2009, 3:73 (17 July 2009) |
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Transcriptional programs: Modelling higher order structure in transcriptional control John E Reid, Sascha Ott, Lorenz Wernisch BMC Bioinformatics 2009, 10:218 (16 July 2009) |
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Method
Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal Genome Biology 2009, 10:R27 (6 March 2009) DISTILLER, a data integration framework for the inference of transcriptional module networks, is presented and used to investigate the condition dependency and modularity in Escherichia coli networks. |
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Research article
Gene set-based module discovery in the breast cancer transcriptome Atsushi Niida, Andrew D Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama BMC Bioinformatics 2009, 10:71 (26 February 2009) |
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Methodology article
Systematic identification of yeast cell cycle transcription factors using multiple data sources Wei-Sheng Wu, Wen-Hsiung Li BMC Bioinformatics 2008, 9:522 (5 December 2008) |
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Research article
Identifying gene regulatory modules of heat shock response in yeast Wei-Sheng Wu, Wen-Hsiung Li BMC Genomics 2008, 9:439 (23 September 2008) |
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Research article
Grace S Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang, Yi-Chen Lo BMC Bioinformatics 2008, 9:134 (3 March 2008) |
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Research article
Prioritization of gene regulatory interactions from large-scale modules in yeast Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron BMC Bioinformatics 2008, 9:32 (22 January 2008) |
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Methodology article
Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah BMC Bioinformatics 2007, 8:454 (18 November 2007) |
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Research article
Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic BMC Bioinformatics 2007, 8:283 (3 August 2007) |
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Research
Validating module network learning algorithms using simulated data Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer BMC Bioinformatics 2007, 8(Suppl 2):S5 (3 May 2007) |
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Method
Clustering of genes into regulons using integrated modeling-COGRIM Guang Chen, Shane T Jensen, Christian J Stoeckert Genome Biology 2007, 8:R4 (4 January 2007) COGRIM, an implementation that integrates gene expression, ChIP binding and transcription factor motif data, is described and applied to both unicellular and mammalian organisms. |