Multiscale characterization of ageing and cancer progression by a novel network entropy measure

Molecular BioSystems

Volumn 11, Issue 7, 2015, Pages 1824-1831

  Menichetti, Giulia ^a   Bianconi, Ginestra ^b   Castellani, Gastone ^a   Giampieri, Enrico ^a   Remondini, Daniel ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AGING; ALGORITHM; BIOLOGICAL MODEL; DISEASE COURSE; ENTROPY; GENE EXPRESSION PROFILING; HUMAN; METABOLISM; NEOPLASM; PATHOLOGY; PROTEIN PROTEIN INTERACTION;

AGING; ALGORITHMS; DISEASE PROGRESSION; ENTROPY; GENE EXPRESSION PROFILING; HUMANS; MODELS, BIOLOGICAL; NEOPLASMS; PROTEIN INTERACTION MAPS;

EID: 84934994553     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c5mb00143a     Document Type: Article

References (29)

1. M. Pagel and A. Pomiankowski, Evolutionary genomics and proteomics, Sinauer Associates, 2008
2. J. De Las Rivas C. Fontanillo Protein-protein interactions essentials: key concepts to building and analyzing interactome networks PLoS Comput. Biol. 2010 6 6 e1000807
3. A.-L. Barabasi Z. N. Oltvai Network biology: understanding the cell's functional organization Nat. Rev. Genet. 2004 5 101 113
4. E. Alm A. Arkin Biological networks Curr. Opin. Struct. Biol. 2003 13 2 193 202
5. M. Vidal M. Cusick A. Barabasi Interactome networks and human disease Cell 2011 144 6 989 998
6. E. Cerami B. Gross E. Demir I. Rodchenkov O. Babur N. Anwar N. Schultz G. Bader C. Sander Pathway commons, a web resource for biological pathway data Nucleic Acids Res. 2011 39 D685 D690
7. D. Szklarczyk A. Franceschini M. Kuhn M. Simonovic A. Roth P. Minguez T. Doerks M. Stark J. Muller P. Bork L. Jensen C. von Mering The string database in 2011: functional interaction networks of proteins, globally integrated and scored Nucleic Acids Res. 2011 39 S1 D561 D568
8. A. Teschendorff S. Severini Increased entropy of signal transduction in the cancer metastasis phenotype BMC Syst. Biol. 2010 4 1 104
9. F. Barea D. Bonatto Aging defined by a chronologic-replicative protein network in saccharomyces cerevisiae: an interactome analysis Mech. Ageing Dev. 2009 130 7 444 460
10. J. West G. Bianconi S. Severini A. Teschendorff Differential network entropy reveals cancer system hallmarks Sci. Rep. 2012 2 802
11. W. N. van Wieringen A. W. van der Vaart Statistical analysis of the cancer cell's molecular entropy using high-throughput data Bioinformatics 2011 27 4 556 563
12. K. Anand G. Bianconi Gibbs entropy of network ensembles by cavity methods Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2010 82 011116
13. G. Bianconi P. Pin M. Marsili Assessing the relevance of node features for network structure PNAS 2009 106 11433 11438
14. B. Gyorffy B. Molnar H. Lage Z. Szallasi A. Ecklund Evaluation of microarray preprocessing algorithms based on concordance with rt-pcr in clinical samples PLoS One 2009 4 e5645
15. K. Scotlandi D. Remondini G. Castellani M. Manara F. Nardi L. Cantiani M. Francesconi M. Mercuri A. Caccuri M. Serra M. Knuutila P. Picci Overcoming resistance to conventional drugs in ewing sarcoma and identification of molecular predictors of outcome J. Clin. Oncol. 2009 27 2209 2216
16. C. Sotiriou P. Wirapati S. Loi A. Harris S. Fox J. Smeds H. Nordgren P. Farmer V. Praz B. Haibe-Kains C. Desmedt D. Larsimont F. Cardoso H. Peterse D. Nuyten M. Buyse M. J. Van de Vijver J. Bergh M. Piccart M. Delorenzi Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis J. Natl. Cancer Inst. 2006 98 4 262 272
17. S. Loi B. Haibe-Kains C. Desmedt F. Lallemand A. M. Tutt C. Gillet P. Ellis A. Harris J. Bergh J. A. Foekens J. G. Klijn D. Larsimont M. Buyse G. Bontempi M. Delorenzi M. J. Piccart C. Sotiriou Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade J. Clin. Oncol. 2007 25 10 1239 1246
18. Y. Wang J. G. Klijn Y. Zhang A. M. Sieuwerts M. P. Look F. Yang D. Talantov M. Timmermans M. E. Meijer-van Gelder J. Yu T. Jatkoe E. M. Berns D. Atkins J. A. Foekens Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer Lancet 2005 365 9460 671 679
19. D. Remondini S. Salvioli M. Francesconi M. Pierini D. J. Mazzatti J. R. Powell I. Zironi F. Bersani G. Castellani C. Franceschi Complex patterns of gene expression in human t cells during in vivo aging Mol. BioSyst. 2010 6 1983 1992
20. G. Bianconi Entropy of network ensembles Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2009 79 036114
21. K. Anand G. Bianconi Entropy measures for networks: Toward an information theory of complex topologies Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2009 80 045102
22. D. Hanahan R. Weinberg The hallmarks of cancer Cell 2000 100 57 70
23. S. Brabletz T. Brabletz The zeb/mir-200 feedback loop - a motor of cellular plasticity in development and cancer? EMBO Rep. 2010 11 9 670 677
24. C. Holohan S. Van Schaeybroeck D. B. Longley P. G. Johnston Cancer drug resistance: an evolving paradigm Nat. Rev. Cancer 2013 13 10 714 726
25. M. Greaves C. C. Maley Clonal evolution in cancer Nature 2012 481 306 313
26. L. Ferrucci F. Giallauria D. Schlessinger Mapping the road to resilience: Novel math for the study of frailty Mech. Ageing Dev. 2008 129 677 679
27. L. Fried L. Ferrucci J. Darer J. Williamson G. Anderson Untangling the concepts of disability, frailty, and comorbidity: Implications for improved targeting and care J. Gerontol. 2004 59 3 255 263
28. E. Bellavista M. Martucci F. Vasuri A. Santoro M. Mishto A. Kloss E. Capizzi A. Degiovanni C. Lanzarini D. Remondini A. Dazzi S. Pellegrini M. Cescon M. Capri S. Salvioli A. D'Errico-Grigionic B. Dahlmannd G. Grazi C. Franceschi Lifelong maintenance of composition, function and cellular/subcellular distribution of proteasomes in human liver Mech. Ageing Dev. 2014 141-142 26 34
29. H. Lempiainen D. Shore Growth control and ribosome biogenesis Curr. Opin. Cell Biol. 2009 21 855 863