Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model

Bioinformatics

Volumn 24, Issue 3, 2008, Pages 404-411

  Wei, Peng J ^a   Pan, Wei T ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR GCN4;

ARTICLE; CORRELATION ANALYSIS; GENE TARGETING; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROBABILITY; STATISTICAL ANALYSIS;

ALGORITHMS; CHROMATIN IMMUNOPRECIPITATION; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; GENE EXPRESSION PROFILING; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; SIGNAL TRANSDUCTION; STATISTICS AS TOPIC;

EID: 38849163722     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm612     Document Type: Article

References (36)

1. Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
2. Beyer,A. et al. (2006) Integrated assessment and prediction of transcription factor binding. PLoS Compul. Biol., 2, e70.
3. Besag,J. (1986) On the statistical analysis of dirty pictures. J. Roy. Stal. Soc.: B, 48, 259-302.
4. Besag,J. and Kooperberg,C. (1995) On conditional and intrinsic autoregressions. Biometrika, 82, 733-746.
5. Broet,P. and Richardson,S. (2006) Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. Biomformatics, 22, 911-918.
6. Congdon,P. (2001) Bayesian Statistical Modelling. Wiley, Chichester.
7. Dopazo,J. (2006) Functional Interpretation of Microarray Experiments. OMICS: J. Int. Biol., 10, 398-410.
8. Efron,B. et al. (2001) Empirical Bayes analysis of a inicroarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
9. Efron,B. and Tibshirani,R. (2007) On testing the significance of sets of genes. Ann. Appl. Stat., 1, 107-129.
10. Elion,E.A., Brill,J.A. and Fink,G.R. (1991) FUS3 represses CLN1 and CLN2 and in concert with KSS1 promotes signal transduction. Proceedings of National Academy of Science, 88, 9392-9396.
11. Fernandez,C. and Green,P. (2002) Modelling spatially correlated data via mixtures: A Bayesian approach. J. Roy. Stat. Soc.: B, 64, 805-826.
12. Franke,L. and van Bakel,H. (2006) Reconstruction of a Functional Human Gene Network, with an Application for Prioritizing Positional Candidate Genes. Am. J. Hum. Genet., 78, 1011-1025.
13. Harbison,C.T. et al. (2004) Transcriptional Regulatory Code of a Eukaryotic, Genome. Nature, 431, 99-104.
14. Jauniax,J.C. et al. (1978) Arginine metabolism in Saccharomyces cerevisiae: Subcellular localization of the enzymes. J. Bacteriol. 133, 1096-1107.
15. Kanehisa,M and Goto,S (2000) Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 17-30.
16. Lee,I. et al. (2004) Probabilistic Functional Network of Yeast Genes. Science, 306, 1555-1558.
17. Lee,T.I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
18. Lewin,A et al. (2006) Bayesian modeling of differential gene expression. Biometrics, 62, 1-9.
19. McLachlan,G.J. et al. (2006) A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays. Bioinformatics, 22, 1608-1615.
20. McLachlan,G.J. and Peel,D. (2006) Finite Mixture Models Wiley, New York.
21. Newton,M.A. et al. (2001) On differential voriability of expression, ratios: Improving statistical inference about gene expression changes from microarray data. J. Comput. Biol., 8 37-52.
22. Newton,M.A. et al. (2007) Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Ann. Appl. Stat., 1, 85-106.
23. Pan,W. et al. (2002) Model-Based Cluster Analysis of Microarray Gene Expression Data. Genome Biol., 3, research0009, 1-8.
24. Pan,W. (2005) Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data. Stat. Appl. Genet. Mol. Biol., 4, Article 12.
25. Pan,W. (2006) Incorporating gene functional annotations in detecting differential gene expression. Appl. Stat., 55, 301-316.
26. Pan,W. (2066b) Incorporating gene functions as priors in model-based clustering of microarray gene expression data. Bioinformatics, 22, 795-801.
27. Pauwels,K. et al. (2003) The N-acetylglutamate synthase/ N-acetylglutamate kinase metabolon of Saccharomyces cerevisiae allows co-ordinated feedback regulation of the first two steps in arginine biosynthesis. Eur. J. Biochem., 270, 1014-1024.
28. Pokholok,D.K. et al. (2005) Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast. Cell, 122, 517-527.
29. Spiegelhalter,D. et al. (2003) WinBUGS User Manual, Version 1.4 Available at http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/manuall4.pdf.
30. Subramanian,A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of National Academy of Science, 102, 15545-15550.
31. Tian,L et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of National Academy of Science, 102, 13544-13549.
32. Toyn,J.H. et al. (2000) A counterselection for the tryptophan pathway in yeast: 5-fluoroanthranilic acid resistance. Yeast, 16, 553-560.
33. Tusher,V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of National Academy of Science, 98, 5116-5121.
34. Wei,P. and Pan,W. (2007) Incorporating Gene Networks into Statistical Tests for Genomic Data via a Spatially Correlated Mixture Model. Research Repon 2007-032. University of Minnesota, Division of Biostatistics, Available at http://www.biostat.umn.edu./rrs.php.
35. Wei,Z. and Li,H. (2007) A Markov Random Field Model for Network-based Analysis of Genomic Data. Bioinformatics, 23, 1537-1544.
36. Yiao,G. et al. (2005) Improved detection of differentially expressed genes through incorporation of gene locations. Research Report 2005-028. University of Minnesota, Division of Biostatistics, Available at http://www.biostat.umn.edu/rrs.php.