A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities

Biostatistics

Volumn 13, Issue 1, 2012, Pages 129-141

  Soneson, Charlotte ^a   Fontes, Magnus ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Exchangeability; Gene ranking; List; Microarray

Indexed keywords

ARTICLE; BIOSTATISTICS; BREAST TUMOR; COMPARATIVE STUDY; DNA MICROARRAY; EVALUATION; FEMALE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; LUNG TUMOR; STATISTICAL ANALYSIS; STATISTICAL MODEL; STATISTICS;

BIOSTATISTICS; BREAST NEOPLASMS; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; HUMANS; LUNG NEOPLASMS; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 83755220000     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxr023     Document Type: Article

References (27)

1. ABEEL, T., HELLEPUTTE, T., VAN DE PEER, Y., DUPONT, P. AND SAEYS, Y. (2010). Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics 26, 392-398.
2. ABRAHAM, G., KOWALCZYK, A., LOI, S., HAVIV, I. AND ZOBEL, J. (2010). Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics 11, 277.
3. ACKERMANN, M. AND STRIMMER, K. (2009). A general modular framework for gene set enrichment analysis. BMC Bioinformatics 10, 47.
4. ALDOUS, D. (1985). Exchangeability and related topics. In: Ećole d'E će de Probabilite de Saint-Flour XIII 1983. Lecture Notes in Mathematics, Volume 1117. Berlin: Springer, pp. 1-198. 10.1007/BFb0099421.
5. BHATTACHARJEE, A., RICHARDS, W. G., STAUNTON, J., LI, C., MONTI, S., VASA, P., LADD, C., BEHESHTI, J., BUENO, R., GILLETTE, M. and others (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proceedings of the National Academy of Sciences of the United States of America 98, 13790-13795. (Pubitemid 33115977)
6. BOULESTEIX, A. L. AND SLAWSKI, M. (2009). Stability and aggregation of ranked gene lists. Briefings in Bioinformatics 10, 556-568.
7. BREITLING, R., ARMENGAUD, P., AMTMANN, A. AND HERZYK, P. (2004). Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Letters 573, 83-92. (Pubitemid 39141040)
8. DECONDE, R. P., HAWLEY, S., FALCON, S., CLEGG, N., KNUDSEN, B. AND ETZIONI, R. (2006). Combining results of microarray experiments: A rank aggregation approach. Statistical Applications in Genetics and Molecular Biology 5, Article 15.
9. DR̂AGHICI, S., KHATRI, P., MARTINS, R. P., OSTERMEIER, G. C. AND KRAWETZ, S. A. (2003). Global functional profiling of gene expression. Genomics 81, 98-104. (Pubitemid 36298600)
10. EFRON, B., TIBSHIRANI, R., STOREY, J. D. AND TUSHER, V. (2001). Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association 96, 1151-1160. (Pubitemid 33695570)
11. EIN-DOR, L., ZUK, O. AND DOMANY, E. (2006). Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proceedings of the National Academy of Sciences of the United States of America 103, 5923-5928.
12. FAN, C., OH, D. S., WESSELS, L., WEIGELT, B., NUYTEN, D. S. A., NOBEL, A. B., VAN'T VEER, L. J. AND PEROU, C. M. (2006). Concordance among gene-expression-based predictors for breast cancer. New England Journal of Medicine 355, 560-569. (Pubitemid 44200649)
13. FORTUNEL, N. O., OTU, H. H., NG, H. H., CHEN, J., MU, X., CHEVASSUT, T., LI, X., JOSEPH, M., BAILEY, C., HATZFELD, J. A. and others (2003). Comment on "'Stemness': Transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature." Science 302, 393b.
14. HE, Z. AND YU, W. (2010). Stable feature selection for biomarker discovery. Computational Biology and Chemistry 34, 215-225.
15. HEDENFALK, I., DUGGAN, D., CHEN, Y., RADMACHER, M., BITTNER, M., SIMON, R., MELTZER, P., GUSTERSON, B., ESTELLER, M., RAFFELD, M. and others (2001). Gene expression profiles in hereditary breast cancer. New England Journal of Medicine 344, 539-548. (Pubitemid 32167867)
16. HONG, F. AND BREITLING, R. (2008). A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 24, 374-382. (Pubitemid 351189013)
17. IRIZARRY, R. A., WARREN, D., SPENCER, F., KIM, I. F., BISWAL, S., FRANK, B. C., GABRIELSON, E., GARCIA, J. G. N., GEOGHEGAN, J., GERMINO, G. and others (2005). Multiple-laboratory comparison of microarray platforms. Nature Methods 2, 345-349. (Pubitemid 41130979)
18. JURMAN, G., MERLER, S., BARLA, A., PAOLI, S., GALEA, A. AND FURLANELLO, C. (2008). Algebraic stability indicators for ranked lists in molecular profiling. Bioinformatics 24, 258-264.
19. JURMAN, G., RICCADONNA, S., VISINTAINER, R. AND FURLANELLO, C. (2010). Algebraic comparison of partial lists in bioinformatics. ArXiv: 1004.1341v1.
20. KINGMAN, J. F. C. (1978). Uses of exchangeability. Annals of Probability 6, 183-197.
21. MICHIELS, S., KOSCIELNY, S. AND HILL, C.(2005). Prediction of cancer outcome with microarrays: A multiple random validation study. The Lancet 365, 488-492. (Pubitemid 40215731)
22. PEPE, M. S., LONGTON, G. M., ANDERSON, G. L. AND SCHUMMER, M. (2003). Selecting differentially expressed genes from microarray experiments. Biometrics 59, 133-142. (Pubitemid 36523116)
23. RHODES, D. R., BARRETTE, T. R., RUBIN, M. A., GHOSH, D. AND CHINNAIYAN, A. M. (2002). Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Research 62, 4427-4433. (Pubitemid 34827303)
24. RHODES, D. R., YU, J., SHANKER, K., DESHPANDE, N., VARAMBALLY, R., GHOSH, D., BARRETTE, T., PANDEY, A. AND CHINNAIYAN, A. M. (2004). Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences of the United States of America 101, 9309-9314. (Pubitemid 38812872)
25. SCHOLKOPF, B. AND SMOLA, A. J. (2002). Learning with Kernels. Cambridge, MA: MIT Press.
26. SUBRAMANIAN, A., TAMAYO, P., MOOTHA, V. K., MUKHERJEE, S., EBERT, B. L., GILLETTE, M. A., PAULOVICH, A., POMEROY, S. C., GOLUB, T. R., LANDER, E. S. and others (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550. (Pubitemid 41528093)
27. TUSHER, V. G., TIBSHIRANI, R. AND CHU, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America 98, 5116-5121. (Pubitemid 32397092)