Literature DB >> 15004292

Comparative evaluation of microarray analysis software.

Daniel K Liu1, Bin Yao, Brian Fayz, David D Womble, Stephen A Krawetz.   

Abstract

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the "ideal microarray analysis software suite."

Mesh：

Year:  2004        PMID： 15004292     DOI： 10.1385/MB:26:3:225

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN： 1073-6085            Impact factor:   2.695


  11 in total

Review 1.  Microarrays under the microscope.

Authors:  S E Wildsmith; F J Elcock
Journal:  Mol Pathol       Date:  2001-02

2.  Profiling gene expression using onto-express.

Authors:  Purvesh Khatri; Sorin Draghici; G Charles Ostermeier; Stephen A Krawetz
Journal:  Genomics       Date:  2002-02       Impact factor: 5.736

Review 3.  A concise guide to cDNA microarray analysis.

Authors:  P Hegde; R Qi; K Abernathy; C Gay; S Dharap; R Gaspard; J E Hughes; E Snesrud; N Lee; J Quackenbush
Journal:  Biotechniques       Date:  2000-09       Impact factor: 1.993

4.  DNA arrays for analysis of gene expression.

Authors:  M B Eisen; P O Brown
Journal:  Methods Enzymol       Date:  1999       Impact factor: 1.600

5.  SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.

Authors:  Maximilian Diehn; Gavin Sherlock; Gail Binkley; Heng Jin; John C Matese; Tina Hernandez-Boussard; Christian A Rees; J Michael Cherry; David Botstein; Patrick O Brown; Ash A Alizadeh
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

6.  Drug target validation and identification of secondary drug target effects using DNA microarrays.

Authors:  M J Marton; J L DeRisi; H A Bennett; V R Iyer; M R Meyer; C J Roberts; R Stoughton; J Burchard; D Slade; H Dai; D E Bassett; L H Hartwell; P O Brown; S H Friend
Journal:  Nat Med       Date:  1998-11       Impact factor: 53.440

Review 7.  Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications.

Authors:  S L Beaucage
Journal:  Curr Med Chem       Date:  2001-08       Impact factor: 4.530

8.  Molecular classification of cutaneous malignant melanoma by gene expression profiling.

Authors:  M Bittner; P Meltzer; Y Chen; Y Jiang; E Seftor; M Hendrix; M Radmacher; R Simon; Z Yakhini; A Ben-Dor; N Sampas; E Dougherty; E Wang; F Marincola; C Gooden; J Lueders; A Glatfelter; P Pollock; J Carpten; E Gillanders; D Leja; K Dietrich; C Beaudry; M Berens; D Alberts; V Sondak
Journal:  Nature       Date:  2000-08-03       Impact factor: 49.962

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

Authors:  Lao H Saal; Carl Troein; Johan Vallon-Christersson; Sofia Gruvberger; Ake Borg; Carsten Peterson
Journal:  Genome Biol       Date:  2002-07-15       Impact factor: 13.583

10.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583
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