Comparative evaluation of microarray analysis software

Applied Biochemistry and Biotechnology - Part B Molecular Biotechnology

Volumn 26, Issue 3, 2004, Pages 225-232

  Liu, Daniel K ^a   Yao, Bin ^a   Fayz, Brian ^a   Womble, David D ^a   Krawetz, Stephen A ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Analysis; Comparison; Microarray; Shareware; Software

Indexed keywords

COMPUTER AIDED SOFTWARE ENGINEERING; COMPUTER SOFTWARE; DATA REDUCTION; PROJECT MANAGEMENT;

COMPARISON; MICROARRAY ANALYSIS; SHARAWARE; SUBSETS;

MOLECULAR BIOLOGY;

ARTIFICIAL NEURAL NETWORK; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; COST; DATA ANALYSIS; DATA BASE; DNA MICROARRAY; EVALUATION; INFORMATION PROCESSING; PRINCIPAL COMPONENT ANALYSIS; QUALITY CONTROL; REVIEW; STATISTICAL ANALYSIS; GENE EXPRESSION PROFILING; METHODOLOGY;

AUTOMATIC DATA PROCESSING; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 16544391306     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1385/MB:26:3:225     Document Type: Review

References (13)

1. Beaucage, S. L. (2001) Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications. Curr. Med. Chem. 8, 1213-1244.
2. Al-Khaldi, S. F., Martin, S. A., Rasooly, A., and Evans, J. D. (2002) DNA microarray technology used for studying foodborne pathogens and microbial habitats: minireview. J. AOAC Int. 85, 906-910.
3. Marton, M. J., DeRisi, J. L., Bennett, H. A., et al. (1998) Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Med. 4, 1293-1301.
4. Draghici, S. (2003) Data analysis and visualization in DNA microarrays. In Introduction to Bioinformatics (Krawetz, S. and Womble, D., eds.). Humana Press, Totowa, NJ, pp. 665-692.
5. Bittner, M., Meltzer, Y., Chen, Y., et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406, 536-540.
6. Eisen, M. B. and Brown, P. O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179-205.
7. Hegde, P., Qi, R., Abernathy, K., et al. (2000) A concise guide to cDNA microarray analysis. Biotechniques 29, 548-556.
8. Gentleman, R. and Carey, V. (2002) Bioconductor. R News 2, 11-16.
9. Saal, L., Troein, C., Vallon-Christersson, J., Gruvberger, S., Borg, A., and Peterson, C. (2002) BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 3, software0003.1-0003.6.
10. Wildsmith, S. E. and Elcock, F. J. (2001) Microarrays under the microscope. Mol. Pathol. 54, 8-16.
11. Spellman, P. T., Miller, M., Stewart, J., et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046.
12. Diehn, M., Sherlock, G., Binkley G., et al. (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31, 219-223.
13. Khatri, P., Draghici, S., Ostermeier, C., and Krawetz, S. (2002) Profiling gene expression using Onto-Express. Genomics 79, 266-270.