Conclusion
Information is the king and knowledge is the queen in this post-genomics era. He who can mine the useful information from the messy raw data and turn it into knowledge is God. The software that helps the mining process is Michael the Archangel who leads the victorious battle against the complex biological problems. If you want to win the battle, start working with your angel now!
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References
Becker KG. (2001). The sharing of cDNA microarray data. Nat Rev Neurosci. 2:438–440.
Brazma A., Vilo J. (2000) Gene expression data analysis. FEBS Lett. 480:17–24.
Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 29:365–371.
D’haeseleer P., Liang S., Somogyi R. (2000). Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16:707–726.
de Jong H. (2002). Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 9:67–103.
Eisen M.B., Spellman P.T., Brown P.O., Botstein D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 95:14863–14868.
Fiehn 0. (2002). Metabolomics—the link between genotypes and phenotypes. Mol Biol. 48:155–171.
Gardiner-Garden M., Littlejohn T.G. (2001), A comparison of microarray databases. Brief Bioinform. 2:143–158.
Geschwind D.H. (2001). Sharing gene expression data: an array of options. Nat Rev Neurosci. 2:435–438.
Grosu P., Townsend J.P., Hartl D.L., Cavalieri D. (2002). Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res. 12:1121–1126.
Hebestreit H.F. (2001). Proteomics: an holistic analysis of nature’s proteins. Curr Opin Pharmacol. 2001; 1:513–520.
Horvath S., Baur M.P. (2000). Future directions of research in statistical genetics. Stat Med. 19:3337–3343.
Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., Kidd M.J., King A.M., Meyer M.R., Slade D., Lum P.Y., Stepaniants S.B., Shoemaker D.D., Gachotte D., Chakraburtty K., Simon J., Bard M., Friend S.H. (2000). Functional discovery via a compendium of expression profiles. Cell. 102:109–26.
Jain A.N., Tokuyasu T.A., Snijders A.M., Segraves R., Albertson D.G., Pinkel D. (2002). Fully automatic quantification of microarray image data. Genome Res. 12:325–332.
Jagota A. (2001). Microarray Data Analysis and Visualization. Bioinformatics by the Bay Press.
Knuden S. (2002). A Biologist’s Guide to Analysis of DNA Microarray Data. New York: John Wiley & Sons, 2002.
Krause A., Olson M. (2000). The Basics of S and S-Plus. New York: Springer Verlag.
Leung Y.F., Lam D.S.C., Pang C.P. (2001). In silico biology: observation, modeling, hypothesis and verification. Trends Genet. 17:622–623.
Leung Y.F. (2002). Microarray data analysis for dummies... and experts too? Trends Biochem Sci. in press.
Leung Y.F., Pang C.P. (2002). Eye on bioinformatics — dissecting complex disease trait in silico. Applied Bioinform., in press.
Leung Y.F., Tam P.O.S., Lee W.S., Yam G.H.F., Chua J.K.H., Lam D.S.C., Pang C.P. (2002). The dual role of dexamethasone on anti-inflammation and outflow resistance in human trabecular meshwork. Submitted.
Lönnstedt I., Speed T.P. (2002). Replicated Microarray Data. Stat Sinica 12:31–46.
Miles M.F. (2001). Microarrays: lost in a storm of data? Nat Rev Neurosci. 2:441–443.
Nadon R., Shoemaker J. (2002). Statistical issues with microarrays: processing and analysis. Trends Genet. 18:265–271.
Phelps T.J., Palumbo A.V., Beliaev A.S. (2002). Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol. 13:20–24.
Quackenbush J. (2001). Computational genetics computational analysis of microarray data. Nat Rev Genet. 2:418–427.
Roberts C.J., Nelson B., Marton M.J., Stoughton R., Meyer M.R., Bennett H.A., He Y.D., Dai H., Walker W.L., Hughes T.R., Tyers M., Boone C., Friend S.H. (2000). Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287:873–880.
Roth F.P., Hughes J.D., Estep P.W., Church G.M. (1998). Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 16:939–945.
Schoeberl B., Eichler-Jonsson C., Gilles E.D., Muller G. (2002). Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol. 20:370–375.
Selvin S. (1998). Modern Applied Biostatistical Methods: Using S-Plus. New York: Oxford University Press.
Sherlock G. (2001). Analysis of large-scale gene expression data. Brief Bioinform. 2:350–362.
Stewart J.E., Mangalam H., Zhou J. (2001). Open Source Software meets gene expression. Brief Bioinform. 2:319–328.
Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., Church G.M. (1999). Systematic determination of genetic network architecture. Nat Genet. 22:281–285.
Tomiuk S., Hofmann K. (2001). Microarray probe selection strategies. Brief Bioinform. 2:329–340.
Venables WN, Ripley BD. (1999). Modern Applied Statistics With S-Plus. New York: Springer Verlag.
Wu T.D. (2001). Analysing gene expression data from DNA microarrays to identify candidate genes. J Pathol 195:53–65.
Yang Y.H., Buckley M.J., Speed T.P. (2001). Analysis of cDNA microarray images. Brief Bioinform 2:341–349.
Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., Speed T.P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:E15.
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Leung, Y.F., Chiu Lam, D.S., Pang1, C.P. (2003). Microarray Software Review. In: Berrar, D.P., Dubitzky, W., Granzow, M. (eds) A Practical Approach to Microarray Data Analysis. Springer, Boston, MA. https://doi.org/10.1007/0-306-47815-3_19
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DOI: https://doi.org/10.1007/0-306-47815-3_19
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