Multilevel support vector regression analysis to identify condition-specific regulatory networks

Bioinformatics

Volumn 26, Issue 11, 2010, Pages 1416-1422

  Chen, Li ^a   Xuan, Jianhua ^a   Riggins, Rebecca B ^b   Wang, Yue ^a   Hoffman, Eric P ^c   Clarke, Robert ^b,d  

^a State University   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c CHILDREN'S NATIONAL MEDICAL CENTER   (United States)

^d GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN;

ARTICLE; BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; METHODOLOGY; REGRESSION ANALYSIS; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ESTROGENS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; REGRESSION ANALYSIS; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

EID: 77953898349     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq144     Document Type: Article

References (51)

1. Aerts, S. et al. (2003) Computational detection of cis-regulatory modules. Bioinformatics, 19 (Suppl. 2), ii5-ii14.
2. Andrew, S.D. et al. (2000) Sp1 and Sp3 transactivate the RET proto-oncogene promoter. Gene, 256, 283-291.
3. Aparicio, O. et al. (2004) Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr. Protoc. Cell Biol., Chapter 17, Unit 17 17.
4. Bar-Joseph, Z. et al. (2003) Computational discovery of gene modules and regulatory networks. Nat. Biotechnol., 21, 1337-1342.
5. Bjornstrom, L. and Sjoberg, M. (2005) Mechanisms of estrogen receptor signaling: convergence of genomic and nongenomic actions on target genes. Mol. Endocrinol., 19, 833-842.
6. Boulay, A. et al. (2008) The Ret receptor tyrosine kinase pathway functionally interacts with the ERalpha pathway in breast cancer. Cancer Res., 68, 3743-3751.
7. Brunner, N. et al. (1997)M CF7/LCC9:a na ntiestrogen-resistant MCF-7 variant in which acquired resistance to the steroidal antiestrogen ICI 182, 780 confers an early cross- resistance to the nonsteroidal antiestrogen tamoxifen. Cancer Res., 57, 3486-3493.
8. Bussemaker, H.J. et al. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
9. Chen, G. et al. (2007) Clustering of genes into regulons using integrated modeling- COGRIM. Genome Biol., 8, R4.
10. Chen, L. et al. (2008) Identification of condition-specific regulatory modules by multi- level motif and mRNA expression analysis. The 2008 International Conference on Bioinformatics and Computational Biology. Las Vegas, Nevada.
11. Clarke, R. et al. (1989) Progression from hormone dependent to hormone independent growth in MCF-7 human breast cancer cells. Proc. Natl Acad. Sci., 86, 3649-3653.
12. Creighton, C.J. et al. (2006) Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors. Genome Biol., 7, R28.
13. Das, D. et al. (2006)Adaptively inferring human transcriptional subnetworks. Mol. Syst. Biol., 2, 2006 0029.
14. Gao, F. et al. (2004) Defining transcriptional networks through integrative modeling of mRNAexpression and transcription factor binding data. BMC Bioinformatics, 5, 31.
15. Gomez, B.P. et al. (2007) Human X-box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines. FASEB J., 21, 4013-4027.
16. Gong, T. et al. (2008) Exploring transcriptional modules by integrative gene clustering guided by transcription factor binding information. The 2008 International Conference on Bioinformatics and Computational Biology. Las Vegas, Nevada.
17. Gu, Z.et al. (2002)Associationofinterferonregulatoryfactor-1, nucleophosmin, nuclear factor-kappaB, and cyclic AMP response element binding with acquired resistance to Faslodex (ICI 182, 780). Cancer Res., 62, 3428-3437.
18. Hayward, P. et al. (2005) Notch modulates Wnt signalling by associating with Armadillo/beta-catenin and regulating its transcriptional activity. Development, 132, 1819-1830.
19. Ihmels, J. et al. (2004) Defining transcription modules using large-scale gene expression data. Bioinformatics, 20, 1993-2003.
20. Imbriano, C. et al. (2005) Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters. Mol. Cell Biol., 25, 3737-3751.
21. Kakizawa, T. et al. (2001) Silencing mediator for retinoid and thyroid hormone receptors interacts with octamer transcription factor-1 and acts as a transcriptional repressor. J. Biol. Chem., 276, 9720-9725.
22. Kim, K. et al. (2003) Domains of estrogen receptor alpha (ERalpha) required for ERalpha/Sp1-mediated activation of GC-rich promoters by estrogens and antiestrogens in breast cancer cells. Mol. Endocrinol., 17, 804-817.
23. Kohonen, T. (1997) Self-Organizing Maps. Springer, NY.
24. Lee, T.I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
25. Liao, J.C. et al. (2003) Network component analysis: reconstruction of regulatory signals in biological systems. Proc. Natl Acad. Sci. USA, 100, 15522-15527.
26. Lomax, R.G. (2007) Statistical Concepts: A Second Course. Lawerence Erlbaum Associates, Mahwah, NJ.
27. Luker, K.E. and Luker, G.D. (2006) Functions of CXCL12 and CXCR4 in breast cancer. Cancer Lett., 238, 30-41.
28. Maere, S. et al. (2005) BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
29. Mishra, G.R. et al. (2006) Human protein reference database-2006 update. NucleicAcids Res., 34, D411-D414.
30. Nguyen, D.H. and D'Haeseleer, P. (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol. Syst. Biol., 2, 2006 0012.
31. Pattarozzi, A. et al. (2008) 17beta-estradiol promotes breast cancer cell proliferation- inducing stromal cell-derived factor-1-mediated epidermal growth factor receptor transactivation: reversal by gefitinib pretreatment. Mol. Pharmacol., 73, 191-202.
32. Pennanen, P.T. et al. (2009) Gene expression changes during the development of estrogen-independent and antiestrogen-resistant growth in breast cancer cell culture models. Anticancer Drugs, 20, 51-58.
33. Pratt, M.A. et al. (2003) Estrogen withdrawal-induced NF-kappaB activity and bcl- 3 expression in breast cancer cells: roles in growth and hormone independence. Mol. Cell Biol., 23, 6887-6900.
34. Qi, Y. and Ge, H. (2006) Modularity and dynamics of cellular networks. PLoS Comput. Biol., 2, e174.
35. Riggins, R.B. et al. (2005) The nuclear factor kappa B inhibitor parthenolide restores ICI 182, 780 (Faslodex; fulvestrant)-induced apoptosis in antiestrogen-resistant breast cancer cells. Mol. Cancer Ther., 4, 33-41.
36. Riggins, R.B. et al. (2008) ERRgamma mediates tamoxifen resistance in novel models of invasive lobular breast cancer. Cancer Res., 68, 8908-8917.
37. Ruan, J. and Zhang, W. (2006)Abi-dimensional regression tree approach to the modeling of gene expression regulation. Bioinformatics, 22, 332-340.
38. Sala, A. et al. (1999) B-MYB transactivates its own promoter through SP1-binding sites. Oncogene, 18, 1333-1339.
39. Segal, E. et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176.
40. Segal, E. et al. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
41. Sharan, R. et al. (2003) CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics, 19 (Suppl. 1), i283-i291.
42. Smola, A.J. and Scholkopf, B. (1998) A tutorial on support vector regression. NeuroCOLT2 Technical Report.
43. Spellman, P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
44. Tibshirani, R. (1996) Regression shrinkage and selection via the lasso. J. Royal Stat. Soc. B, 58, 267-288.
45. Tusher, V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
46. Van den Bulcke, T. et al. (2006) SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics, 7, 43.
47. Wang, W. et al. (2005) Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc. Natl Acad. Sci. USA, 102, 1998-2003.
48. Xing, W. andArcher, T.K. (1998)U pstream stimulatory factors mediate estrogen receptor activation of the cathepsin D promoter. Mol. Endocrinol., 12, 1310-1321.
49. Yu, T. and Li, K.C. (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics, 21, 4033-4038.
50. Zhou, Q. and Wong, W.H. (2004) CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad. Sci. USA, 101, 12114-12119.
51. Zhou, Y. et al. (2007) Enhanced NF kappa B andAP-1 transcriptional activity associated with antiestrogen resistant breast cancer. BMC Cancer, 7, 59.