Causal reasoning on biological networks: Interpreting transcriptional changes

Bioinformatics

Volumn 28, Issue 8, 2012, Pages 1114-1121

  Chindelevitch, Leonid ^a   Ziemek, Daniel ^a   Enayetallah, Ahmed ^a   Randhawa, Ranjit ^a   Sidders, Ben ^b   Brockel, Christoph ^a   Huang, Enoch S ^a  

^a PFIZER INC   (United States)

^b PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; BREAST TUMOR; CARDIOMEGALY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METHODOLOGY;

ALGORITHMS; BREAST NEOPLASMS; CARDIOMEGALY; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; MODELS, BIOLOGICAL;

EID: 84859748911     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts090     Document Type: Article

References (19)

1. Aragno, M. et al. (2008) Oxidative stress triggers cardiac fibrosis in the heart of diabetic rats. Endocrinology, 149, 380-388.
2. Aslanian, A. et al. (2004) Repression of the arf tumor suppressor by e2f3 is required for normal cell cycle kinetics. Gene. Dev., 18, 1413-1422.
3. Bild, A.H. et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439, 353-357.
4. Chen, H.-Z. et al. (2009) Emerging roles of e2fs in cancer: an exit from cell cycle control. Nat. Rev. Cancer, 9, 785-797.
5. der Heiden, K.V. et al. (2010) Role of nuclear factor kappab in cardiovascular health and disease.Clin. Sci., 118, 593-605.
6. Draghici, S. et al. (2003) Global functional profiling of gene expression. Genomics, 81, 98-104.
7. Galindo, C.L. et al. (2009) Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure. BMC Physiol., 9, 23.
8. Hartemink, A.J. et al. (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.Pac. Symp. Biocomput., 422-433.
9. Kanehisa, M. et al. (2010) Kegg for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
10. Petkovšek, M. et al. (1996) A=B. Wellesley, MA: A K Peters.
11. Pollard, J. et al. (2005) A computational model to define the molecular causes of type 2 diabetes mellitus. Diabetes Technol. Ther., 7, 323-336.
12. Rao, A.R. et al. (1996) A Markov chain Monte Carlo method for generating random (0, 1)-matrices with given marginals. Indian J. Stat., 58, 225-242.
13. Rona, G. (1985) Catecholamine cardiotoxicity. J. Mol. Cell. Cardiol., 17, 291-306.
14. Schadt, E.E. et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet., 37, 710-717.
15. Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
16. Suganuma, M. et al. (1999) Essential role of tumor necrosis factor alpha (TNF-alpha) in tumor promotion as revealed by TNF-alpha-deficient mice. Cancer Res., 59, 4516-4518.
17. Teekakirikul, P. et al. (2010) Cardiac fibrosis in mice with hypertrophic cardiomyopathy is mediated by non-myocyte proliferation and requires tgf-beta. J. Clin. Invest., 120, 3520-3529.
18. Wölkart, G. et al. (2006) Role of endogenous hydrogen peroxide in cardiovascular ischaemia/reperfusion function: studies in mouse hearts with catalaseoverexpression in the vascular endothelium. Pharmacol. Res., 54, 50-56.
19. Zien, A. et al. (2000) Analysis of gene expression data with pathway scores. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 407-417.