Have a personal or library account? Click to login

The Stability of Gene Selection in Microarray Experiments

Open Access
|Dec 2013

References

  1. Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., Tranchevent, L. C., De Moor, B., Marynen, P., Hassan, B., Carmeliet, P., & Moreau, Y. (2006). Gene prioritization through genomic data fusion. Nat Biotechnol, 24, 537-544.10.1038/nbt1203
  2. Boulesteix, A. L., & Slawski, M. (2009). Stability and aggregation of ranked gene lists. Brief Bioinformatics, 10, 556-568.10.1093/bib/bbp034
  3. Boulesteix, A. L., Strobl, C., Augustin, T., & Daumer, M. (2008). Evaluating Microarray-based Classifiers: An Overview. Cancer Informatics, 6, 77-97.10.4137/CIN.S408
  4. Chen, C., Mendez, E., Houck, J., Fan,W., Lohavanichbutr, P., Doody, D., Yueh, B., Futran, N. D., Upton, M., Farwell, D. G., Schwartz, S. M., & Zhao, L. P. (2008). Gene expression profiling identifies genes predictive of oral squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev, 17(8), 2152-2162.10.1158/1055-9965.EPI-07-2893
  5. Efron, B., & Tibshirani, R. (2002). Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol, 23, 70-86.10.1002/gepi.1124
  6. Irizarry, R. A.,Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S. C., Hoffman, E., Jedlicka, A. E., Kawasaki, E., Martinez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., Quackenbush, J., Scott, A., Wilson, M., Yang, Y., Ye, S. Q., & Yu, W. (2005). Multiple-laboratory comparison of microarray platforms. Nat Methods, 2, 345-350.10.1038/nmeth756
  7. Mas, V. R., Maluf, D. G., Archer, K. J., Yanek, K., Kong, X., Kulik, L., Freise, C. E., Olthoff, K. M., Ghobrial, R. M., McIver, P., & Fisher, R. A. (2009). Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma. Mol Med, 15(3-4), 85-94.10.2119/molmed.2008.00110
  8. Public Repository ArrayExpress. (2013). Transcription profiling by array of whole blood samples from colorectal cancer patients and healthy individuals, accession number E-MTAB-1532. Retrieved from http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1532/.
  9. Public Repository Gene Expression Omnibus. (2009). RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver, accession number GSE1423. Retrieved from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14323.
  10. Public Repository Gene Expression Omnibus. (2011). Gene expression profiling of oral squamous cell carcinoma (OSCC), accession number GSE30784. Retrieved from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30784.
  11. Smyth, G. K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol, 3(1). DOI: 10.2202/1544-6115.1027.10.2202/1544-6115.1027
  12. Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98(9), 5116-5121.10.1073/pnas.091062498
  13. Van Sanden, S., Lin, D., & Burzykowski, T. (2008). Performance of gene selection and classification methods in a microarray setting: A simulation study. Communications in Statistics - Simulation and Computation, 37(2), 409-424.10.1080/03610910701792554
  14. Xu, Y., Xu, Q., Yang, L., Ye, X., Liu, F., Wu, F., Ni, S., Tan, C., Cai, G., Meng, X., Cai, S., & Du, X. (2013). Identification and Validation of a Blood-Based 18- Gene Expression Signature in Colorectal Cancer. Clin Cancer Res, 19(11), 3039-3049.10.1158/1078-0432.CCR-12-3851
  15. Zhang, M., Zhang, L., Zou, J., Yao, Ch., Xiao, H., Liu, Q., Wang, J., Wang, D., Wang, Ch., & Guo, Z. (2009). Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlatedmolecular changes. Bioinformatics, 25(13), 1662-1668. 10.1093/bioinformatics/btp295
DOI: https://doi.org/10.2478/slgr-2013-0040 | Journal eISSN: 2199-6059 | Journal ISSN: 0860-150X
Language: English
Page range: 87 - 101
Published on: Dec 31, 2013
Published by: University of Białystok, Department of Pedagogy and Psychology
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Related subjects:

© 2013 Magdalena Wietlicka-Piszcz, published by University of Białystok, Department of Pedagogy and Psychology
This work is licensed under the Creative Commons License.