A mixture model for the evolution of gene expression in non-homogeneous datasets

Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference

Volumn , Issue , 2009, Pages 1297-1304

  Quon, Gerald ^a   Teh, Yee Whye ^b   Chan, Esther ^a   Hughes, Timothy ^a   Brudno, Michael ^a   Morris, Quaid ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; CONSERVATION;

BROWNIAN; EUKARYOTIC ORGANISMS; GENES EXPRESSION; MICROARRAY DATASET; MIXTURE MODELING; NON-HOMOGENEOUS; PHYLOGENETIC ANALYSIS; PROBABILISTIC MODELS; SIMPLE++; STATISTIC MODELING;

GENE EXPRESSION;

EID: 84858769355     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. Li,W., Yang, J., Gu, X. (2005) Expression divergence between duplicate genes. Trends Genet., 21, 602-607. (Pubitemid 41429288)
2. Chen, K., Rajewsky, N. (2007) The evolution of gene regulation by transcription factors and microRNAs. Nature Rev. Genet., 8, 93-103. (Pubitemid 46122839)
3. Yergeau, D.A. et al. (2005) bloodthirsty, an RBCC/TRIM gene required for erythropoiesis in zebrafish. Dev. Biol., 283, 97-112. (Pubitemid 40834329)
4. Stuart, J.M., Segal, E., Koller, D., Kim, S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255. (Pubitemid 37248749)
5. Tirosh, I., Weinberger, A., Carmi, M., Barkai, N. (2006) A genetic signature of interspecies variations in gene expression. Nat. Genet., 38, 830-834. (Pubitemid 43980606)
6. Khaitovich, P. et al. (2005) A neutral model of transcriptome evolution. PLoS. Biol., 2, 682-689.
7. Ghahramani, Z., & Hinton, G.E. (1996) The EM algorithm for mixtures of factor analyzers. Technical Report CRG-TR-96-2, University of Toronto.
8. Gu, X. (2004) Statistical framework for phylogenomic analysis of gene family expression profiles. Genetics, 167, 531-542. (Pubitemid 38736408)
9. Oakley, T.H. et al. (2005) Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Mol. Biol. Evol., 22, 40-50. (Pubitemid 39642234)
10. Felsenstein, J. (2004) Inferring phylogenies. Sunderland (Massachusetts): Sinauer Associates. 664 p.
11. Felsenstein, J. (1981) Evolutionary trees from gene-frequencies and quantitative characters - finding maximum likelihood estimates. Evolution, 35, 1229-1242.
12. Khaitovich et al. (2006) Evolution of primate gene expression. Nat. Rev. Genet., 7, 693-702. (Pubitemid 44260005)
13. Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol., 39, 306-314. (Pubitemid 24283346)
14. Kardong, K.V. (2006) Vertebrates: comparative anatomy, function, evolution. McGraw-Hill. 782 p.
15. Zhang, W., Morris, Q.D. et al. (2004) The functional landscape of mouse gene expression. J. Biol., 3, 21.
16. Huber, W. et al. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18, S96-104. (Pubitemid 41185642)
17. The Gene Ontology Consortium. (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
18. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797. (Pubitemid 38832724)
19. Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591. (Pubitemid 47236688)