| 1. |
Augenlicht, L. H., Wahrman, M. Z., Halsey, H., Anderson, L., Taylor, J., and Lipkin, M. (1987) Expression of cloned sequences
in biopsies of human colonic tissue and in colonic carcinoma cells induced to differentiate in vitro. Cancer Res.
47, 6017–6021.
|
| |
| 2. |
Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature
409, 860–921.
|
| |
| 3. |
Brazma, A., Hingamp, P., Quackenbush, J., et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards
for microarray data. Nat. Genet.
29, 365–371.
|
| |
| 4. |
Dodson, J. M., Charles, P. T., Stenger, D. A., and Pancrazio, J. J. (2002) Quantitative assessment of filter-based cDNA microarrays:
gene expression profiles of human T-lymphoma cell lines. Bioinformatics
18, 953–960.
|
| |
| 5. |
Li, Q., Fraley, C., Bumgarner, R.E., Yeung, K.Y., and Raftery, A.E. (2005) In: “Technical Report no. 473” (http://www.stat.washington.edu/www/research/reports/ 2005/tr473.pdf, Ed.), University of Washington, Seattle.
|
| |
| 6. |
Jain, A. N., Tokuyasu, T. A., Snijders, A. M., Segraves, R., Albertson, D. G., and Pinkel, D. (2002) Fully automatic quantification
of microarray image data. Genome Res.
12, 325–332.
|
| |
| 7. |
Quackenbush, J. (2002) Microarray data normalization and transformation. Nat Genet
32(Suppl), 496–501.
|
| |
| 8. |
Zien, A., Aigner, T., Zimmer, R., and Lengauer, T. (2001) Centralization: a new method for the normalization of gene expression
data. Bioinformatics
17(Suppl 1), S323–S331.
|
| |
| 9. |
Yang, Y. H., Dudoit, S., Luu, P., et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing
single and multiple slide systematic variation. Nucleic Acids Res.
30, e15.
|
| |
| 10. |
Kepler, T. B., Crosby, L., and Morgan, K. T. (2002) Normalization and analysis of DNA microarray data by self-consistency
and local regression. Genome Biol.
3, RESEARCH0037.
|
| |
| 11. |
Zhao, Y., Li, M. C., and Simon, R. (2005) An adaptive method for cDNA microarray normalization. BMC Bio informatics
6, 28.
|
| |
| 12. |
Sasik, R., Calvo, E., and Corbeil, J. (2002) Statistical analysis of high-density oligonucleotide arrays: a multiplicative
noise model. Bioinformatics
18, 1633–1640.
|
| |
| 13. |
Li, H., Wood, C. L., Getchell, T. V., Getchell, M. L., and Stromberg, A. J. (2004) Analysis of oligonucleotide array experiments
with repeated measures using mixed models. BMC Bioinformatics
5, 209.
|
| |
| 14. |
Meuwissen, T. H., and Goddard, M. E. (2004) Bootstrapping of gene-expression data improves and controls the false discovery
rate of differentially expressed genes. Genet. Sel. Evol.
36, 191–205.
|
| |
| 15. |
Reiner, A., Yekutieli, D., and Benjamini, Y. (2003) Identifying differentially expressed genes using false discovery rate
controlling procedures. Bioinformatics
19, 368–375.
|
| |
| 16. |
Barrett, T., Suzek, T. O., Troup, D. B., et al. (2005) NCBI GEO: mining millions of expression profiles — database and tools.
Nucleic Acids Res.
33 Database Issue, D562–D566.
|
| |
| 17. |
Sherlock, G. (2000) Analysis of large-scale gene expression data. Curr. Opin. Immunol.
12, 201–205.
|
| |
| 18. |
Wang, J., Delabie, J., Aasheim, H., Smeland, E., and Myklebost, O. (2002) Clustering of the SOM easily reveals distinct gene
expression patterns: results of a reanalysis of lymphoma study. BMC Bioinformatics
3, 36.
|
| |
| 19. |
Dharmadi, Y, and Gonzalez, R. (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems.
Biotechnol. Prog.
20, 1309–1324.
|
| |
| 20. |
Bittner, M., Meltzer, P., Chen, Y, et al. (2000) Molecular classification of cutaneous malignant melanoma by gene expression
profiling. Nature
406, 536–540.
|
| |
| 21. |
Ramaswamy, S., Tamayo, P., Rifkin, R., et al. (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl. Acad. Sei. USA
98, 15,149–15,154.
|
| |
| 22. |
Cunliffe, H. E., Ringner, M., Bilke, S., et al. (2003) The gene expression response of breast cancer to growth regulators:
patterns and correlation with tumor expression profiles. Cancer Res.
63, 7158–7166.
|
| |
| 23. |
Burczynski, M. E., Oestreicher, J. L., Cahilly, M. J., et al. (2005) Clinical pharmacogenomics and transcriptional profiling
in early phase oncology clinical trials. Curr. Mol. Med.
5, 83–102.
|
| |
| 24. |
Nutt, C. L., Mani, D. R., Betensky, R. A., et al. (2003) Gene expression-based classification of malignant gliomas correlates
better with survival than histological classification. Cancer Res.
63, 1602–1607.
|
| |
| 25. |
Mendez, M. A., Hodar, C., Vulpe, C., Gonzalez, M., and Cambiazo, V. (2002) Discriminant analysis to evaluate clustering of
gene expression data. FEBS Lett.
522, 24–28.
|
| |
| 26. |
Olshen, A. B., and Jain, A. N. (2002) Deriving quantitative conclusions from microarray expression data. Bioinformatics
18, 961–970.
|
| |
| 27. |
Brown, M. P., Grundy, W. N., Lin, D., et al. (2000) Knowledge-based analysis of microarray gene expression data by using support
vector machines. Proc. Natl. Acad. Sei. USA
97, 262–267.
|
| |
| 28. |
Khan, J., Wei, J. S., Ringner, M., et al. (2001) Classification and diagnostic prediction of cancers using gene expression
profiling and artificial neural networks. Nat Med
7, 673–679.
|
| |
| 29. |
Ringner, M., Peterson, C., and Khan, J. (2002) Analyzing array data using supervised methods. Pharmacogenomics
3, 403–415.
|
| |
| 30. |
Zhang, H., Yu, C. Y., Singer, B., and Xiong, M. (2001) Recursive partitioning for tumor classification with gene expression
microarray data. Proc. Natl. Acad. Sci. USA
98, 6730–6735.
|
| |
| 31. |
Zeeberg, B. R., Feng, W., Wang, G., et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic
data. Genome Biol.
4, R28.
|
| |
| 32. |
Dennis, G.,Jr., Sherman, B. T., Hosack, D. A., et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated
Discovery. Genome Biol.
4, P3.
|
| |
| 33. |
Demir, E., Babur, O., Dogrusoz, U., et al. (2002) PATIKA: an integrated visual environment for collaborative construction
and analysis of cellular pathways. Bioinformatics
18, 996–1003.
|
| |
| 34. |
Raponi, M., Belly, R. T., Karp, J. E., Lancet, J. E., Atkins, D., and Wang, Y (2004) Microarray analysis reveals genetic pathways
modulated by tipifarnib in acute myeloid leukemia. BMC Cancer
4, 56.
|
| |
| 35. |
Jenson, S. D., Robetorye, R. S., Bohling, S. D., et al. (2003) Validation of cDNA microarray gene expression data obtained
from linearly amplified RNA. Mol. Pathol.
56, 307–312.
|
| |
| 36. |
Winer, J., Jung, C. K., Shackel, I., and Williams, P. M. (1999) Development and validation of real-time quantitative reverse
transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem.
270, 41–49.
|
| |
| 37. |
Kononen, J., Bubendorf, L., Kallioniemi, A., et al. (1998) Tissue microarrays for high-throughput molecular profiling of tumor
specimens. Nat. Med.
4, 844–847.
|
| |