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PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.

Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H.

BMC Bioinformatics. 2003 Nov 7;4:56.


GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W.

Plant Physiol. 2004 Sep;136(1):2621-32. Erratum in: Plant Physiol. 2004 Dec;136(4):4335.


MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters.

Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK.

BMC Genomics. 2008 Feb 28;9:105. doi: 10.1186/1471-2164-9-105.


Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble CA, Oliver SG, Kell DB.

BMC Bioinformatics. 2008 Aug 7;9:334. doi: 10.1186/1471-2105-9-334.


The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P.

Nucleic Acids Res. 2003 Jan 1;31(1):224-8.


Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

Naika M, Shameer K, Sowdhamini R.

Mol Biosyst. 2013 Jul;9(7):1888-908. doi: 10.1039/c3mb70072k. Epub 2013 May 3.


CressExpress: a tool for large-scale mining of expression data from Arabidopsis.

Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE.

Plant Physiol. 2008 Jul;147(3):1004-16. doi: 10.1104/pp.107.115535. Epub 2008 May 8.


EXPath: a database of comparative expression analysis inferring metabolic pathways for plants.

Chien CH, Chow CN, Wu NY, Chiang-Hsieh YF, Hou PF, Chang WC.

BMC Genomics. 2015;16 Suppl 2:S6. doi: 10.1186/1471-2164-16-S2-S6. Epub 2015 Jan 21.


Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

Stenger JE, Xu H, Haynes C, Hauser ER, Pericak-Vance M, Goldschmidt-Clermont PJ, Vance JM.

BMC Bioinformatics. 2005 Apr 12;6:95.


Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

Guzzi PH, Cannataro M.

Comput Methods Programs Biomed. 2013 Aug;111(2):402-9. doi: 10.1016/j.cmpb.2013.04.006. Epub 2013 May 31.


Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

Wada M, Takahashi H, Altaf-Ul-Amin M, Nakamura K, Hirai MY, Ohta D, Kanaya S.

Gene. 2012 Jul 15;503(1):56-64. doi: 10.1016/j.gene.2012.04.043. Epub 2012 Apr 24.


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

Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WG, Gilmartin PM, Westhead DR.

Plant J. 2006 Apr;46(2):336-48.


MARS: microarray analysis, retrieval, and storage system.

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z.

BMC Bioinformatics. 2005 Apr 18;6:101.


MetaCyc and AraCyc. Metabolic pathway databases for plant research.

Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY.

Plant Physiol. 2005 May;138(1):27-37.


Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications.

Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P.

Plant Mol Biol. 2005 May;58(2):229-45.


The PowerAtlas: a power and sample size atlas for microarray experimental design and research.

Page GP, Edwards JW, Gadbury GL, Yelisetti P, Wang J, Trivedi P, Allison DB.

BMC Bioinformatics. 2006 Feb 22;7:84.


Data mining in the MetaCyc family of pathway databases.

Karp PD, Paley S, Altman T.

Methods Mol Biol. 2013;939:183-200. doi: 10.1007/978-1-62703-107-3_12.

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