Bioinformatics Advance Access originally published online on June 4, 2004
Bioinformatics 2004 20(17):3246-3248; doi:10.1093/bioinformatics/bth349
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.
Applications Note |
Java Treeview—extensible visualization of microarray data
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Received on May 20, 2004; accepted on May 25, 2004
Advance Access Publication June 4, 2004
Summary: Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.
Availability: http://jtreeview.sourceforge.net under GPL.
Contact: alokito{at}users.sourceforge.net
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E. L. Greer, P. R. Oskoui, M. R. Banko, J. M. Maniar, M. P. Gygi, S. P. Gygi, and A. Brunet The Energy Sensor AMP-activated Protein Kinase Directly Regulates the Mammalian FOXO3 Transcription Factor J. Biol. Chem., October 12, 2007; 282(41): 30107 - 30119. [Abstract] [Full Text] [PDF]
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X. Tang, J. Gal, X. Zhuang, W. Wang, H. Zhu, and G. Tang A simple array platform for microRNA analysis and its application in mouse tissues RNA, October 1, 2007; 13(10): 1803 - 1822. [Abstract] [Full Text] [PDF]
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T. L. Lee, X. P. Yang, B. Yan, J. Friedman, P. Duggal, L. Bagain, G. Dong, N. T. Yeh, J. Wang, J. Zhou, et al. A Novel Nuclear Factor-{kappa}B Gene Signature Is Differentially Expressed in Head and Neck Squamous Cell Carcinomas in Association with TP53 Status Clin. Cancer Res., October 1, 2007; 13(19): 5680 - 5691. [Abstract] [Full Text] [PDF]
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L. Wu, S.-I. Hwang, K. Rezaul, L. J. Lu, V. Mayya, M. Gerstein, J. K. Eng, D. H. Lundgren, and D. K. Han Global Survey of Human T Leukemic Cells by Integrating Proteomics and Transcriptomics Profiling Mol. Cell. Proteomics, August 1, 2007; 6(8): 1343 - 1353. [Abstract] [Full Text] [PDF]
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D. Sahoo, D. L. Dill, R. Tibshirani, and S. K. Plevritis Extracting binary signals from microarray time-course data Nucleic Acids Res., June 28, 2007; 35(11): 3705 - 3712. [Abstract] [Full Text] [PDF]
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M. Nicolau, R. Tibshirani, A.-L. Borresen-Dale, and S. S. Jeffrey Disease-specific genomic analysis: identifying the signature of pathologic biology Bioinformatics, April 15, 2007; 23(8): 957 - 965. [Abstract] [Full Text] [PDF]
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A. E. Platts, D. J. Dix, H. E. Chemes, K. E. Thompson, R. Goodrich, J. C. Rockett, V. Y. Rawe, S. Quintana, M. P. Diamond, L. F. Strader, et al. Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs Hum. Mol. Genet., April 1, 2007; 16(7): 763 - 773. [Abstract] [Full Text] [PDF]
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S. R. Collins, P. Kemmeren, X.-C. Zhao, J. F. Greenblatt, F. Spencer, F. C. P. Holstege, J. S. Weissman, and N. J. Krogan Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae Mol. Cell. Proteomics, March 1, 2007; 6(3): 439 - 450. [Abstract] [Full Text] [PDF]
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S S Cross, R F Harrison, S P Balasubramanian, J M Lippitt, C A Evans, M W R Reed, and I Holen Expression of receptor activator of nuclear factor {kappa}{beta} ligand (RANKL) and tumour necrosis factor related, apoptosis inducing ligand (TRAIL) in breast cancer, and their relations with osteoprotegerin, oestrogen receptor, and clinicopathological variables J. Clin. Pathol., July 1, 2006; 59(7): 716 - 720. [Abstract] [Full Text] [PDF]
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V. D. Pham, C. W. Shebelut, I. R. Jose, D. A. Hodgson, D. E. Whitworth, and M. Singer The response regulator PhoP4 is required for late developmental events in Myxococcus xanthus Microbiology, June 1, 2006; 152(6): 1609 - 1620. [Abstract] [Full Text] [PDF]
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C. J. Creighton, A. M. Hilger, S. Murthy, J. M. Rae, A. M. Chinnaiyan, and D. El-Ashry Activation of Mitogen-Activated Protein Kinase in Estrogen Receptor {alpha}-Positive Breast Cancer Cells In vitro Induces an In vivo Molecular Phenotype of Estrogen Receptor {alpha}-Negative Human Breast Tumors. Cancer Res., April 1, 2006; 66(7): 3903 - 3911. [Abstract] [Full Text] [PDF]
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Z. Fei, X. Tang, R. Alba, and J. Giovannoni Tomato Expression Database (TED): a suite of data presentation and analysis tools Nucleic Acids Res., January 1, 2006; 34(suppl_1): D766 - D770. [Abstract] [Full Text] [PDF]
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B. C. Foat, S. S. Houshmandi, W. M. Olivas, and H. J. Bussemaker Profiling condition-specific, genome-wide regulation of mRNA stability in yeast PNAS, December 6, 2005; 102(49): 17675 - 17680. [Abstract] [Full Text] [PDF]
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K. Dolinski and D. Botstein Changing perspectives in yeast research nearly a decade after the genome sequence Genome Res., December 1, 2005; 15(12): 1611 - 1619. [Abstract] [Full Text] [PDF]
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A. Sarver and J. DeRisi Fzf1p Regulates an Inducible Response to Nitrosative Stress in Saccharomyces cerevisiae Mol. Biol. Cell, October 1, 2005; 16(10): 4781 - 4791. [Abstract] [Full Text] [PDF]
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