Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer

Bioinformatics

Volumn 22, Issue 19, 2006, Pages 2396-2404

  Reverter, Antonio ^a   Ingham, Aaron ^a   Lehnert, Sigrid A ^a   Tan, Siok Hwee ^a   Wang, Yonghong ^a   Ratnakumar, Abhirami ^a   Dalrymple, Brian P ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE;

ADIPOGENESIS; ARTICLE; CORRELATION ANALYSIS; COW; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC DATABASE; HUMAN; IN VITRO STUDY; INFLAMMATION; MALIGNANT NEOPLASTIC DISEASE; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SERIAL ANALYSIS OF GENE EXPRESSION; STATISTICAL DISTRIBUTION;

BOS TAURUS;

EID: 33749988857     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl392     Document Type: Article

References (43)

1. Amenta,P.S. et al. (2000) Type XV collagen in human colonic adenocarcinomas has a different distribution than other basement membrane zone proteins. Hum. Pathol., 31, 359-366.
2. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
3. Blais,A. and Dynlacht,B.D. (2005) Constructing transcriptional regulatory networks. Genes Dev., 19, 1499-1511.
4. Boon,K. et al. (2002) An anatomy of normal and malignant gene expression. Proc. Natl Acad. Sci. USA, 99, 11287-11292.
5. Bowie,A. and O'Neill,L.A. (2000) The interleukin-1 receptor/Toll-like receptor super-family: Signal generators for pro-inflammatory interleukins and microbial products. J. Leukoc. Biol., 67, 508-514.
6. Brownstein,B.H. et al. (2006) Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury. Physiol. Genomics, 24, 298-309.
7. Calvano,S.E. et al. (2005) A network-based analysis of systemic inflammation in humans. Nature, 437, 1032-1037.
8. Caraux,G. and Pinloche,S. (2005) PermutMatrix: A graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics, 21, 1280-1281.
9. Chatterjee-Kishore,M. and Miller,C.P. (2005) Exploring the sounds of silence: RNAi-mediated gene silencing for target identification and validation. Drug Discov. Today, 10, 1559-1565.
10. Choi,J.K. et al. (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics, 21, 4348-4355.
11. Deng,J. et al. (2000) Activation of signal transducer and activator of transcription-3 during proliferative phases of 3T3-L1 adipogenesis. Endocrinology, 141, 2370-2376.
12. Draghici,S. et al. (2003) Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res., 31, 3775-3781.
13. Efron,B. et al. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
14. Gao,H. et al. (2003) DNA sequence specificity for Topoisomerase II poisoning by the Quinoxaline anticancer drugs XK469 and CQS. Mol. Pharmacol., 63, 1382-1388.
15. Gu,Z. et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature, 421, 31-32.
16. Harp,J.B. et al. (2001) Differential expression of signal transducer and activators of transcription during human adipogenesis. Biochem. Biophys. Res. Commun., 281, 907-912.
17. Jongeneel,C.V. et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res., 15, 1007-1014.
18. Kawai,T. et al. (1999) Unresponsiveness of MyD88-deficient mice to endotoxin. Immunity, 11, 115-122.
19. Khatri,P. et al. (2005) Recent additions and improvements to the onto-tools. Nucleic Acids Res., 33, W762-W765.
20. Lehnert,S.A. et al. (2004) Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. Aust. J. Exp. Agric., 44, 1127-1133.
21. Luscombe,N.M. et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
22. Margulies,E.H. et al. (2001) Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Res., 29, e60.
23. McLachlan,G.J. et al. (2002) A mixture model-based approach to clustering of microarray expression data. Bioinformatics, 18, 413-422.
24. McLachlan,G.J. et al. (2006) A simple implementation of the normal mixture approach to differential gene expression in multiclass microarrays. Bioinformatics, 22, 1608-1615.
25. Odom,D.T. et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science, 303, 1378-1381.
26. Poltorak,A. et al. (1998) Defective LPS signaling in C3H/HeJ and C57BL/ 10ScCr mice: Mutations in Tlr4 gene. Science, 282, 2085-2088.
27. Ramoni,M. et al. (2002) Cluster analysis of gene expression dynamics. Proc. Natl Acad. Sci. USA, 99, 9121-9126.
28. Remondini,D. et al. (2005) Targetting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression dynamics. Proc. Natl Acad. Sci. USA, 102, 6902-6906.
29. Reverter,A. et al. (2004) Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle. J. Anim. Sci., 82, 3430-3439.
30. Reverter,A. et al. (2005a) Validation of alternative methods of data normalization in gene co-expression studies. Bioinformatics, 21, 1112-1120.
31. Reverter,A. et al. (2005b) A rapid method for computationally inferring transcriptomes coverage and microarray sensitivity. Bioinformatics, 21, 80-89.
32. Sasaki,H. et al. (2004) Decreased Hrad6B expression in lung cancer. Acta Oncol., 43, 585-589.
33. Searle,S.R., Casella,G. and McCulloch,C.E. (1992) Variance Components. Wiley, New York.
34. Smith,V. et al. (1997) Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science, 275, 464-464.
35. Stern,M.D. et al. (2003) Can transcriptome size be estimated from SAGE catalogs? Bioinformatics, 19, 443-448.
36. Talwar,S. et al. (2006) Gene expression profiles of peripheral blood leukocytes after endotoxin challenge in human. Physiol. Genomics, 25, 203-215.
37. Tan,S.-H. et al. (2006) Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray. Funct. Integr. Genomics, 6, 235-249.
38. Tusher,V.G. et al. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
39. van Noort,V. et al. (2003) Predicting gene function by conserved co-expression. Trends Genet., 19, 238-242.
40. Wagner,A. (2000) The role of pleiotropy, population size fluctuations, and fitness effects of mutations in the evolution of redundant gene function. Genetics, 154, 1389-1401.
41. Winter,E.E. et al. (2004) Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res., 14, 54-61.
42. Wolfe,C.J. et al. (2005) Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics, 6, 227.
43. Zhang,F.X. et al. (1999) Bacterial lipopolysaccharide activates nuclear factor-kappa B through interleukin-1 signaling mediators in cultured human dermal endothelial cells and mononuclear phagocytes. J. Biol. Chem., 274, 7611-7614.