Correlation Network Analysis and Knowledge Integration

Applied Statistics for Network Biology: Methods in Systems Biology

Volumn 1, Issue , 2011, Pages 251-280

  Plasterer, Thomas N ^a,b   Stanley, Robert ^c   Gombocz, Erich ^c  

^a NORTHEASTERN UNIVERSITY   (United States)

^b Pharmacogenetics Clinical Advisory Board   (United States)

^c IO Informatics Inc   (United States)

Author keywords

Correlation network analysis; Integral informatics; Knowledge annotation; Semantic web; Systems biology

Indexed keywords

EID: 84879993212     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527638079.ch12     Document Type: Chapter

References (55)

1. Oltvai, Z.N. and Barabasi, A.L. (2002) Systems biology. Life's complexity pyramid. Science, 298, 763-764.
2. Schreiber, M., Sugihara, M. et al. (2006) Quantum mechanical studies on the crystallographic model of bathorhodopsin. Angew. Chem. Int. Ed. Engl., 45, 4274-4277.
3. Behrenfeld, M.J., Westberry, T.K. et al. (2009) Satellite-detected fluorescence reveals global physiology of ocean phytoplankton. Biogeosciences, 6, 779-794.
4. van der Greef, J., Martin, S. et al. (2007) The art and practice of systems biology in medicine: mapping patterns of relationships. J. Proteome Res., 6, 1540-1559.
5. Ito, T., Chiba, T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad Sci. USA, 98, 4569-4574.
6. Giot, L., Bader, J.S. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
7. Li, S., Armstrong, C.M. et al. (2004)A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
8. Rual, J.F., Venkatesan, K. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
9. Stelzl, U.,Worm, U. et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968.
10. Krogan, N.J., Cagney, G. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
11. Lee, T.I., Rinaldi, N.J. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
12. Medini, D., Covacci, A. et al. (2006) Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems. PLoS Comput. Biol., 2, e173.
13. Wingender, E., Chen, X. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
14. Qiu, P. (2003) Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem. Biophys. Res. Commun., 309, 495-501.
15. Ekins, S., Nikolsky, Y. et al. (2007) Pathway mapping tools for analysis of high content data.Methods Mol. Biol., 356, 319-350.
16. Ganter, B. and Giroux, C.N. (2008) Emerging applications of network and pathway analysis in drug discovery and development. Curr. Opin. Drug Discov. Devel., 11, 86-94.
17. Ganter, B., Zidek, N. et al. (2008) Pathway analysis tools and toxicogenomics reference databases for risk assessment. Pharmacogenomics, 9, 35-54.
18. Oresic, M., Clish, C.B. et al. (2004) Phenotype characterisation using integrated gene transcript, protein and metabolite profiling. Appl. Bioinformatics, 3, 205-217.
19. Adourian, A., Jennings, E. et al. (2008) Correlation network analysis for data integration and biomarker selection. Mol. BioSyst., 4, 249-259.
20. Adourian, A., Plasterer, T.N. et al. (2009) Systems pharmacology, biomarkers, and biomolecular networks, in Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools, vol. 1 (eds S. Ekins and J.J. Xu), John Wiley & Sons, Inc., Hoboken, NJ, pp. 75-113.
21. McBurney, R.N., Hines,W.M. et al. (2009) The liver toxicity biomarker study: phase I design and preliminary results. Toxicol. Pathol., 37, 52-64.
22. Tim, B.-L., Hendler, J., and Lassila, O. (2001) The Semantic Web. Scientific American Magazine.
23. W3C (2002) Feature Synopsis for OWL Lite and OWL: W3C Working Draft 29 July 2002. http://www.w3.org/TR/ 2002/WD-owl-features-20020729/.
24. W3C (2004) OWLWeb Ontology Language Overview: W3C Recommendation 10 February 2004. http://www.w3.org/TR/owl-features/, http://www.w3.org/TR/2004/REC-owlfeatures- 20040210/
25. Hollander, M. and Wolfe, D.A. (1973) Nonparametric Statistical Inference, John Wiley & Sons, Inc., New York.
26. Schnohr, P., Jensen, G. et al. (1977) The Copenhagen City Heart Study. A prospective cardiovascular population study of 20,000 men and women. Ugeskr. Laeger, 139, 1921-1923.
27. Schnohr, P., Jensen, J.S. et al. (2002) Coronary heart disease risk factors ranked by importance for the individual and community. A 21 year follow-up of 12 000 men and women from The Copenhagen City Heart Study. Eur. Heart. J., 23, 620-626.
28. Best, D.J. and Roberts, D.E. (1975) Algorithm AS 89: the upper tail probabilities of Spearman's rho. Appl. Stat., 24, 377-379.
29. Butte, A.J. and Kohane, I.S. (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput., 418-429.
30. Gardner, T.S., di Bernardo, D. et al. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301, 102-105.
31. di Bernardo, D., Thompson, M.J. et al. (2005) Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat. Biotechnol., 23, 377-383.
32. Yan, A.T., Yan, R.T. et al. (2008) Relationships between plasma levels of matrix metalloproteinases and neurohormonal profile in patients with heart failure. Eur. J. Heart Fail, 10, 125-128.
33. Shannon, P., Markiel, A. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
34. Christmas, R., Avila-Campillo, I. et al. (2005) Cytoscape: a software environment for integrated models of biomolecular interaction networks, AACR Educ. Book, 12-16.
35. Cline, M.S., Smoot, M. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
36. Gao, J., Ade, A.S. et al. (2009) Integrating and annotating the interactome using the MiMI plugin for Cytoscape. Bioinformatics, 25, 137-138.
37. Thiene, G. and Basso, C. (2010) Myocardial infarction: a paradigm of success in modern medicine. Cardiovasc. Pathol., 19, 1-5.
38. Racunas, S.A., Shah, N.H. et al. (2004) HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics, 20 (Suppl. 1), i257-i264.
39. Maglott, D., Ostell, J. et al. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 35, D26-D31.
40. McKusick, V.A. (1998) Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders, Johns Hopkins University Press, Baltimore, MD.
41. Bernstein, F.C., Koetzle, T.F. et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
42. Benson, D.A., Boguski, M.S. et al. (1999) GenBank. Nucleic Acids Res., 27, 12-17.
43. Wu, C.H., Yeh, L.S. et al. (2003) The protein information resource. Nucleic Acids Res., 31, 345-347.
44. Pruitt, K.D., Tatusova, T. et al. (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
45. Bolton, E.E., Wang, Y. et al. (2008) PubChem: integrated platform of small molecules and biological activities. Annu. Rep. Comput. Chem., 4, 217-241.
46. Consortium, U. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
47. Jain, E., Bairoch, A. et al. (2009) Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics, 10, 136.
48. Wishart, D.S., Tzur, D. et al. (2007) HMDB: the Human Metabolome Database. Nucleic Acids Res., 35, D521-D526.
49. Wishart, D.S., Knox, C. et al. (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res., 37, D603-D610.
50. Kanehisa, M., Goto, S. et al. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
51. Ashburner, M., Ball, C.A. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
52. Berardini, T., Li, D. et al. (2010) The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Res., 38, D331-D335.
53. Twigger, S.N., Shimoyama, M. et al. (2007) The Rat Genome Database, update 2007 - easing the path from disease to data and back again. Nucleic Acids Res., 35, D658-D662.
54. Storey, J.D. (2002) A direct approach to false discovery rates. J.R. Statist. Soc., 64, 479-498.
55. Royer, L.C., Reimann, M. et al. (2008) Unraveling protein networks with power graph analysis. PLoS Comput. Biol., 4, e1000108.