The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis

The Plant Journal : for Cell and Molecular Biology
Chih-Hung JenDavid R Westhead

Abstract

We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel clique finder tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots, and dissection into cliques of co-regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co-expression patterns. To demonstra...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jul 19, 2000·The Plant Cell·G BlancM Delseny
Aug 10, 2000·Cell·T R HughesS H Friend
Sep 1, 2000·FEBS Letters·A Brazma, J Vilo
Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·P M SchenkJ M Manners
Dec 16, 2000·Science·T J VisionS D Tanksley
Oct 3, 2001·Microbes and Infection·A Brazma, J Vilo
Oct 13, 2001·Plant Physiology·A BarakatJ Bailey-Serres
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gert ThijsYves Moreau
Oct 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Peter BreyneMarc Zabeau
Jan 7, 2003·Plant & Cell Physiology·Monika S DoblinDeborah P Delmer
Jan 10, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Jan 10, 2003·Nucleic Acids Research·Alvis BrazmaSusanna-Assunta Sansone
Jan 10, 2003·Nucleic Acids Research·Jeremy GollubGavin Sherlock
Jan 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Neil G TaylorSimon R Turner
Nov 18, 2003·The Plant Journal : for Cell and Molecular Biology·Min Seok BaeOhkmae K Park
Dec 19, 2003·Nucleic Acids Research·David J CraigonSean May
Apr 22, 2004·The Plant Cell·Frank WellmerElliot M Meyerowitz
May 12, 2004·Current Opinion in Plant Biology·Wolf-Rüdiger Scheible, Markus Pauly
May 15, 2004·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Takeshi ObayashiHiroyuki Ohta
Jun 3, 2004·Plant Physiology·Tanya Z BerardiniSeung Y Rhee
Jul 13, 2004·Bioinformatics·Dirk SteinhauserJoachim Kopka
Sep 18, 2004·Plant Physiology·Philip ZimmermannWilhelm Gruissem
Sep 28, 2004·The Plant Journal : for Cell and Molecular Biology·Iain W ManfieldWilliam G T Willats
Nov 13, 2004·Genome Biology·David Honys, David Twell
Jun 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Staffan PerssonChristopher R Somerville
Jun 18, 2005·The Plant Journal : for Cell and Molecular Biology·Kiana ToufighiNicholas J Provart

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Citations

Oct 1, 2011·Functional & Integrative Genomics·Mikhail A Kutuzov, Alexandra V Andreeva
Dec 22, 2010·Journal of Experimental Botany·Stéphanie M SwarbreckDimah Z Habash
Dec 7, 2006·Nucleic Acids Research·Claudia GaluschkaReinhard Hehl
Jul 18, 2006·Nucleic Acids Research·Iain W ManfieldDavid R Westhead
May 16, 2008·Nucleic Acids Research·Marek MutwilStaffan Persson
Nov 28, 2012·Nucleic Acids Research·Yutaka SatoYoshiaki Nagamura
Dec 7, 2007·The Plant Cell·Réka Albert
Dec 23, 2009·BMC Bioinformatics·Damion NeroGloria M Coruzzi
Nov 23, 2006·BMC Bioinformatics·Michael Watson
Sep 5, 2009·BMC Systems Biology·Chris J NeedhamDavid R Westhead
Jan 8, 2009·Taiwanese Journal of Obstetrics & Gynecology·Shing-Jyh ChangHsei-Wei Wang
Jan 5, 2010·Taiwanese Journal of Obstetrics & Gynecology·Tao-Yeuan WangHsei-Wei Wang
Dec 28, 2007·Trends in Plant Science·Kazuki SaitoKeiko Yonekura-Sakakibara
Jun 15, 2007·The Plant Journal : for Cell and Molecular Biology·Daniel H GonzalezEduardo F Mufarrege
Dec 2, 2009·The Plant Journal : for Cell and Molecular Biology·James R BradfordDavid R Westhead
Dec 2, 2009·The Plant Journal : for Cell and Molecular Biology·Erik AlexanderssonUrban Johanson
May 13, 2020·BMC Medical Genomics·Apostolos MalatrasWilliam J Duddy
Aug 13, 2021·IScience·Vasileios L ZogopoulosIoannis Michalopoulos

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