Extracting the abstraction pyramid from complex networks

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Cheng, Chia Ying ^a   Hu, Yuh Jyh ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMOUNT OF INFORMATION; EXTRACT INFORMATIONS; GENETIC INTERACTION; METABOLIC PATHWAYS; MULTI-LEVEL HIERARCHIES; PROTEIN-PROTEIN INTERACTION NETWORKS; REAL WORLD SITUATIONS; VERTICAL RELATIONSHIPS;

ABSTRACTING; ITERATIVE METHODS; KNOWLEDGE REPRESENTATION; LARGE SCALE SYSTEMS; PROTEINS;

COMPLEX NETWORKS;

PROTEIN;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; ESCHERICHIA COLI; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; CLUSTER ANALYSIS; ESCHERICHIA COLI; INFORMATION STORAGE AND RETRIEVAL; METABOLIC NETWORKS AND PATHWAYS; PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 77955118003     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-411     Document Type: Article

References (36)

1. Barabasi AL, Oltvai ZN. Network biology: Understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-U115. 10.1038/nrg1272, 14735121.
2. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: Simple building blocks of complex networks. Science 2002, 298(5594):824-827. 10.1126/science.298.5594.824, 12399590.
3. Oltvai ZN, Barabasi AL. Life's complexity pyramid. Science 2002, 298(5594):763-764. 10.1126/science.1078563, 12399572.
4. Sales-Pardo M, Guimera R, Moreira AA, Amaral LAN. Extracting the hierarchical organization of complex systems. Proc Natl Acad Sci USA 2007, 104(39):15224-15229. 10.1073/pnas.0703740104, 2000510, 17881571.
5. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402(6761):C47-C52. 10.1038/35011540, 10591225.
6. Winther R. Varieties of modules: kinds, levels, origins, and behaviors. Journal of Experimental Zoology 2001, 291(2):116-129. 10.1002/jez.1064, 11479913.
7. Rives A, Galitski T. Modular organization of cellular networks. Proceedings of the National Academy of Sciences 2003, 100(3):1128.
8. Wang X, Dalkic E, Wu M, Chan C. Gene module level analysis: identification to networks and dynamics. Current opinion in biotechnology 2008, 19(5):482-491. 10.1016/j.copbio.2008.07.011, 2615490, 18725293.
9. Xue H, Xian B, Dong D, Xia K, Zhu S, Zhang Z, Hou L, Zhang Q, Zhang Y, Han J. A modular network model of aging. Mol Syst Biol 2007, 3(1). 2174624, 18059442.
10. Gagneur J, Krause R, Bouwmeester T, Casari G. Modular decomposition of protein-protein interaction networks. Genome Biol 2004, 5(8). 10.1186/gb-2004-5-8-r57, 507882, 15287979.
11. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 2002, 297(5586):1551-1555. 10.1126/science.1073374, 12202830.
12. Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006, 103(23):8577-8582. 10.1073/pnas.0601602103, 1482622, 16723398.
13. Newman MEJ, Girvan M. Finding and evaluating community structure in networks. Phys Rev E 2004, 69(2).
14. Luo F, Yang YF, Chen CF, Chang R, Zhou JZ, Scheuermann RH. Modular organization of protein interaction networks. Bioinformatics 2007, 23(7):916-916.
15. Radicchi F, Castellano C, Cecconi F, Loreto V, Parisi D. Defining and identifying communities in networks. Proc Natl Acad Sci USA 2004, 101(9):2658-2663. 10.1073/pnas.0400054101, 365677, 14981240.
16. Kitano H. Systems biology: A brief overview. Science 2002, 295(5560):1662-1664. 10.1126/science.1069492, 11872829.
17. Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30(1):42-46. 10.1093/nar/30.1.42, 99091, 11752249.
18. Ertel A, Verghese A, Byers S, Ochs M, Tozeren A. Pathway-specific differences between tumor cell lines and normal and tumor tissue cells. Molecular Cancer 2006, 5(1):55. 10.1186/1476-4598-5-55, 1635729, 17081305.
19. Zhao J, Ding G, Tao L, Yu H, Yu Z, Luo J, Cao Z, Li Y. Modular co-evolution of metabolic networks. Bmc Bioinformatics 2007, 8(1):311. 10.1186/1471-2105-8-311, 2001200, 17723146.
20. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature genetics 2003, 34(2):166-176. 10.1038/ng1165, 12740579.
21. Girvan M, Newman MEJ. Community structure in social and biological networks. Proc Natl Acad Sci USA 2002, 99(12):7821-7826. 10.1073/pnas.122653799, 122977, 12060727.
22. Xu R, Wunsch DC. Clustering 2009, New Jersey: IEEE Press.
23. Barrat A, Barthelemy M, Pastor-Satorras R, Vespignani A. The architecture of complex weighted networks. Proceedings of the National Academy of Sciences 2004, 101(11):3747.
24. Wagner G, Pavlicev M, Cheverud J. The road to modularity. Nat Rev Genet 2007, 8(12):921-931. 10.1038/nrg2267, 18007649.
25. Fodor J. The modularity of mind: An essay on faculty psychology 1983, Cambridge Massachusetts: The MIT Press.
26. Sandige R. Digital design essentials 2002, New Jersey: Prentice Hall.
27. Murtagh F. A survey of recent advances in hierarchical-clustering algorithms. Comput J 1983, 26(4):354-359.
28. Ihmels J, Bergmann S, Berman J, Barkai N. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 2005, 1(3):e39. 10.1371/journal.pgen.0010039, 1239936, 16470937.
29. Ye Y, Godzik A. Comparative analysis of protein domain organization. Genome research 2004, 14(3):343. 10.1101/gr.1610504, 535408, 14993202.
30. Zhang SH, Jin GX, Zhang XS, Chen LN. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007, 7(16):2856-2869. 10.1002/pmic.200700095, 17703505.
31. Chua H, Sung W, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22(13):1623. 10.1093/bioinformatics/btl145, 16632496.
32. Brun C, Chevenet F, Martin D, Wojcik J, Guenoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 2004, 5(1):6-6.
33. Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci USA 2003, 100(22):12579-12583. 10.1073/pnas.2132527100, 240660, 14566057.
34. Zahn CT. Graph-theoretical methods for detecting and describing Gestalt clusters. IEEE T Comput 1971, C-20(1):68-86.
35. Tumminello M, Aste T, Di Matteo T, Mantegna RN. A tool for filtering information in complex systems. Proc Natl Acad Sci USA 2005, 102(30):10421-10426. 10.1073/pnas.0500298102, 1180754, 16027373.
36. Song CM, Havlin S, Makse HA. Origins of fractality in the growth of complex networks. Nat Phys 2006, 2(4):275-281.