Probabilities of spurious connections in gene networks: Application to expression time series

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 1121-1128

  Bickel, David R ^a,b  

^a MEDICAL COLLEGE OF GEORGIA   (United States)

^b PIONEER HI BRED INTERNATIONAL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ANALYTICAL ERROR; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOINFORMATICS; COMPUTER PROGRAM; GENE CONSTRUCT; GENE EXPRESSION; HYPOTHESIS; INTERNET; PRIORITY JOURNAL; PROBABILITY; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; RELIABILITY; TIME SERIES ANALYSIS;

EID: 16344387892     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti140     Document Type: Article

References (22)

1. Agrawal,H. (2002) Extreme self-organization in networks constructed from gene expression data. Phys. Rev. Lett., 89, 268702-1-268702-4.
2. Benjamini,Y. and Hochberg,Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289 300.
3. Bickel,D.R. (2003) Robust cluster analysis of microarray gene expression data with the number of clusters determined biologically. Bioinformatics, 19, 818-824.
4. Bickel,D.R. (2004a) Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes. Bioinformatics, 20, 682-688.
5. Bickel,D.R. (2004b) Error-rate and decision-theoretic methods of multiple testing: which genes have high objective probabilities of differential expression? Stat. Appl. Genet. Mol. Biol., 3, 8.
6. Bickel,D.R. (2004c) On 'Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates': does a large number of tests obviate confidence intervals of the FDR? arXiv.org e-print q-bio.GN/0404032.
7. Breiman,L. (1992) Probability. Society for Industrial and Applied Mathematics, Philadelphia.
8. Butte,A.J., Tamayo,P., Slonim,D., Golub,T.R. and Kohane,I.S. (2000) Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl Acad. Sci. USA, 97, 12182-12186.
9. De Jong,H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol., 9, 67-103.
10. Efron,B. and Tibshirani,R. (1993) An Introduction to the Bootstrap. Chapman & Hall/CRC Press, New York.
11. Efron,B. and Tibshirani,R. (2002) Empirical Bayes methods and false discovery rates for microaarays. Genet. Epidemiol., 23, 70-86.
12. Efron,B., Tibshirani,R., Storey,J.D. and Tusher,V. (2001) Empirical Bayes analysis of a microarray experiment. J Am. Stat. Assoc., 96, 1151-1160.
13. Fernando,R.L., Nettleton,D., Southey,B.R., Dekkers,J.C.M., Rothschild,M.F. and Soller,M. (2004) Controlling the proportion of false positives (PFP) in multiple dependent tests. Genetics, 166, 611-619.
14. Genovese,C. and Wasserman,L. (2002) Operating characteristics and extensions of the false discovery rate procedure. J. R. Stat. Soc. Ser. B, 64, 499-517.
15. Herrmann,C., Berthélemy,M. and Provero,P. (2003) Connectivity distribution of spatial networks. Phys. Rev. E, 68 026128-1-026128-6.
16. Kellam,P., Liu,X., Martin,N., Orengo,C., Swift,S. and Tucker,A. (2002) A framework for modeling virus gene expression data. Intell. Data Anal., 6, 265-279.
17. Müller,P., Parmigiani,G., Robert,C. and Rousseau,J. (2004) Optimal sample size for multiple testing: the case of gene expression microarrays. J. Am. Stat. Assoc., 99, 990-1001.
18. Pepe,M.S., Longton,G., Anderson,G.L. and Schummer,M. (2003) Selecting differentially expressed genes from microarray experiments. Biometrics, 59, 133-142.
19. Development Core Team (2003) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN: 3-900051-00-3.
20. Rho,K., Jeong,H. and Kahng,B. (2003) Identification of essential and functionally modulated genes through the microarray assay. preprint, arXiV.org e-print.
21. Storey,J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. Ser B, 64, 479-498.
22. Storey,J.D. (2003) The positive false discovery rate: a Bayesian interpretation and the Q-value. Ann. Stat. 31, 2013-2035.