Literature DB >> 12186655

BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

Lao H Saal1, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Ake Borg, Carsten Peterson.   

Abstract

The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.

Entities:  

Mesh：

Year:  2002        PMID： 12186655      PMCID： PMC139402          DOI： 10.1186/gb-2002-3-8-software0003

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  23 in total

1.  J-Express: exploring gene expression data using Java.

Authors:  B Dysvik; I Jonassen
Journal:  Bioinformatics       Date:  2001-04       Impact factor: 6.937

2.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.

Authors:  V R Iyer; C E Horak; C S Scafe; D Botstein; M Snyder; P O Brown
Journal:  Nature       Date:  2001-01-25       Impact factor: 49.962

Review 3.  Navigating gene expression using microarrays--a technology review.

Authors:  A Schulze; J Downward
Journal:  Nat Cell Biol       Date:  2001-08       Impact factor: 28.824

Review 4.  Computational analysis of microarray data.

Authors:  J Quackenbush
Journal:  Nat Rev Genet       Date:  2001-06       Impact factor: 53.242

5.  Gene-expression profiles in hereditary breast cancer.

Authors:  I Hedenfalk; D Duggan; Y Chen; M Radmacher; M Bittner; R Simon; P Meltzer; B Gusterson; M Esteller; O P Kallioniemi; B Wilfond; A Borg; J Trent; M Raffeld; Z Yakhini; A Ben-Dor; E Dougherty; J Kononen; L Bubendorf; W Fehrle; S Pittaluga; S Gruvberger; N Loman; O Johannsson; H Olsson; G Sauter
Journal:  N Engl J Med       Date:  2001-02-22       Impact factor: 91.245

6.  cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene.

Authors:  J Khan; M L Bittner; L H Saal; U Teichmann; D O Azorsa; G C Gooden; W J Pavan; J M Trent; P S Meltzer
Journal:  Proc Natl Acad Sci U S A       Date:  1999-11-09       Impact factor: 11.205

7.  Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns.

Authors:  S Gruvberger; M Ringnér; Y Chen; S Panavally; L H Saal; M Fernö; C Peterson; P S Meltzer
Journal:  Cancer Res       Date:  2001-08-15       Impact factor: 12.701

8.  Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks.

Authors:  J Khan; J S Wei; M Ringnér; L H Saal; M Ladanyi; F Westermann; F Berthold; M Schwab; C R Antonescu; C Peterson; P S Meltzer
Journal:  Nat Med       Date:  2001-06       Impact factor: 53.440

9.  RESOURCERER: a database for annotating and linking microarray resources within and across species.

Authors:  J Tsai; R Sultana; Y Lee; G Pertea; S Karamycheva; V Antonescu; J Cho; B Parvizi; F Cheung; J Quackenbush
Journal:  Genome Biol       Date:  2001       Impact factor: 13.583

10.  Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.

Authors:  B B Haab; M J Dunham; P O Brown
Journal:  Genome Biol       Date:  2001-01-22       Impact factor: 13.583
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  150 in total

1.  wCLUTO: a Web-enabled clustering toolkit.

Authors:  Matthew D Rasmussen; Mukund S Deshpande; George Karypis; James Johnson; John A Crow; Ernest F Retzel
Journal:  Plant Physiol       Date:  2003-10       Impact factor: 8.340

2.  LIMaS: the JAVA-based application and database for microarray experiment tracking.

Authors:  Sarah C Webb; Anthony Attwood; Tony Brooks; Tom Freeman; Phil Gardner; Clare Pritchard; Debbie Williams; Peter Underhill; Mark A Strivens; Andy Greenfield; Ekaterina Pilicheva
Journal:  Mamm Genome       Date:  2004-09       Impact factor: 2.957

Review 3.  Comparative evaluation of microarray analysis software.

Authors:  Daniel K Liu; Bin Yao; Brian Fayz; David D Womble; Stephen A Krawetz
Journal:  Mol Biotechnol       Date:  2004-03       Impact factor: 2.695

4.  A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication.

Authors:  Nolwenn Le Meur; Guillaume Lamirault; Audrey Bihouée; Marja Steenman; Hélène Bédrine-Ferran; Raluca Teusan; Gérard Ramstein; Jean J Léger
Journal:  Nucleic Acids Res       Date:  2004-10-08       Impact factor: 16.971

5.  Comparison of transcript profiling on Arabidopsis microarray platform technologies.

Authors:  Jeffrey D Pylatuik; Pierre R Fobert
Journal:  Plant Mol Biol       Date:  2005-07       Impact factor: 4.076

6.  Isolates with low-level vancomycin resistance associated with persistent methicillin-resistant Staphylococcus aureus bacteremia.

Authors:  Benjamin P Howden; Paul D R Johnson; Peter B Ward; Timothy P Stinear; John K Davies
Journal:  Antimicrob Agents Chemother       Date:  2006-09       Impact factor: 5.191

Review 7.  Storage and retrieval of microarray data and open source microarray database software.

Authors:  Gavin Sherlock; Catherine A Ball
Journal:  Mol Biotechnol       Date:  2005-07       Impact factor: 2.695

Review 8.  Bioinformatics and cancer: an essential alliance.

Authors:  Joaquín Dopazo
Journal:  Clin Transl Oncol       Date:  2006-06       Impact factor: 3.405

9.  Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrAB, which encodes methionine sulfoxide reductase.

Authors:  Ishara C Gunesekere; Charlene M Kahler; Catherine S Ryan; Lori A S Snyder; Nigel J Saunders; Julian I Rood; John K Davies
Journal:  J Bacteriol       Date:  2006-05       Impact factor: 3.490

10.  Identification of a transcriptional fingerprint of estrogen exposure in rainbow trout liver.

Authors:  Abby D Benninghoff; David E Williams
Journal:  Toxicol Sci       Date:  2007-09-06       Impact factor: 4.849
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