Biomolecular network querying: A promising approach in systems biology

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Zhang, Shihua ^a,b   Zhang, Xiang Sun ^a   Chen, Luonan ^c,d,e,f  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHANGHAI UNIVERSITY   (China)

^d OSAKA SANGYO UNIVERSITY   (Japan)

^e JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^f INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; EDITORIAL; HUMAN; SEQUENCE ALIGNMENT; SYSTEMS BIOLOGY;

ANIMALS; HUMANS; SEQUENCE ALIGNMENT; SYSTEMS BIOLOGY;

EID: 39549096223     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-5     Document Type: Article

References (38)

1. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M: Interrelating different types of genomic data, from proteome to secretome: Coming in on function. Genome Res 2001, 11:1463-8. 10.1101/gr.207401 11544189
2. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE: A human protein-protein interaction network: A resource for annotating the proteome. Cell 2005, 122(6):957-68. 10.1016/j.cell.2005.08.029 16169070
3. Wang R Wang Y Wu L-Y Zhang X-S Chen L Analysis on Multi-domain Cooperation for Predicting Protein-Protein Interactions BMC Bioinformatics 2007 8 391 doi:10.1186/1471-2105-8-391 10.1186/ 1471-2105-8-391 17937822
4. Basso K: Reverse engineering of regulatory networks in human B cells. Nat Genet 2005, 37:382-390. 10.1038/ng1532 15778709
5. Wang Y, Joshi J, Xu D, Zhang X-S, Chen L: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics 2006, 22:2413-2420. 10.1093/bioinformatics/btl396 16864593
6. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS: Discovering Functional Relationships Between RNA Expression and Chemotherapeutic Susceptibility Using Relevance Networks. Proc Natl Acad Sci USA 2000, 97:12182-12186. 17315 11027309 10.1073/pnas.220392197
7. Carter S, Brechbuler C, MGriffin Bond A: Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 2004, 20(14):2242-2250 10.1093/bioinformatics/ bth234 15130938
8. Zhang B, Horvath S: A General Framework for Weighted Gene Co-Expression Network Analysis. Statistical Applications in Genetics and Molecular Biology 2005, 4(1):17. 10.2202/1544-6115.1128
9. Wang R, Wang Y, Zhang X-S, Chen L: Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics 2007. 10.1093/ bioinformatics/btm465
10. Albert R: Scale-free networks in cell biology. J Cell Sci 2005, 118:4947-4957. 10.1242/jcs.02714 16254242
11. Barabasi A,UOltvai Z: Network biology: understanding the cell's functional organization. Nature Rev Gen 2004, 5:101-113. 10.1038/nrg1272
12. Zhang S, Jin G, Zhang XS, Chen L: Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007, 7(16):2856-2869. 10.1002/pmic.200700095 17703505
13. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555. 10.1126/science.1073374 12202830
14. Alon U: NeTwork motifs: theory and experimental approaches. Nature Rev Genet 2007, 8:450-461. 10.1038/nrg2102
15. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature 2001, 411:41. 10.1038/35075138 11333967
16. Horvath S, Zhang B, Carlson M, Lu K, Zhu S, Felciano R, Laurance M, Zhao W, Shu Q, Lee Y, Scheck A, Liau L, Wu H, Geschwind D, Febbo P, Kornblum H, Cloughesy T, Nelson S, Mischel P: Analysis of oncogenic signaling networks in Glioblastoma identifies ASPM as a novel molecular target. Proc Natl Acad Sci USA 2006, 103(46):17402-17407. 1635024 17090670 10.1073/pnas.0608396103
17. Oldham M, Horvath S, Geschwind D: Conservation and evolution of gene co-expression networks in human and chimpanzee brain. Proc Natl Acad Sci USA 2006, 103(47):17973-8. 1693857 17101986 10.1073/pnas.0605938103
18. Sharan R, Ideker T: Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006, 24:427-433. 10.1038/nbt1196 16601728
19. Sharan R, Ideker T, Kelley B, Shamir R, Karp RM: Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 2005, 12:835-846. 10.1089/ cmb.2005.12.835 16108720
20. Kelley BP, Sharan R, Karp R, Sittler ET, Root DE, Stockwell BR, Ideker T: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 2003, 100:11394-11399. 208768 14504397 10.1073/pnas.1534710100
21. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T: Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 2005, 102:1974-1979. 548573 15687504 10.1073/pnas.0409522102
22. Kelley PB, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T: PathBLAST: A tool for alignment of protein interaction networks. Nucl Acids Res 2004, 32:83-88. 10.1093/nar/gkh411
23. Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M: Alignment of metabolic pathways. Bioinformatics 2005, 21:3401-3408. 10.1093/ bioinformatics/bti554 15985496
24. Trusina A, Sneppen K, Dodd IB, Shearwin KE, Egan JB: Functional alignment of regulatory networks: A study of temperate phages. Plos Comput Biol 2005, 1:e74. 1317652 16477325 10.1371/journal.pcbi.0010074
25. Berg J, Läsig M: Local graph alignment and motif search in biological networks. Proc Natl Acad Sci USA 2004, 101:14689-14694. 522014 15448202 10.1073/pnas.0305199101
26. Koyutürk M, Grama A, Szpankowski W: Pairwise localalignment of protein interaction network guided by models of evolution. RECOM LNBI 2005, 3500:48-65.
27. Ogata H, Fujibuchi W, Goto S, Kanehisa M: A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucl Acids Res 2000, 28:4021-4028. 110779 11024183 10.1093/nar/ 28.20.4021
28. Berg J, Läsig M: Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 2006, 103:10967-10972. 1544158 16835301 10.1073/pnas.0602294103
29. Li Z, Zhang S, Wang Y, Zhang XS, Chen L: Alignment of molecular networks by integer quadratic programming. Bioinformatics 2007, 23(13):1631-1639. 10.1093/bioinformatics/btm156 17468121
30. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S: Graemlin: General and robust alignment of multiple large interaction networks. Genome Res 2006, 16:1169-1181. 1557769 16899655 10.1101/gr.5235706
31. Suthram S, Sittler T, Ideker T: The Plasmodium protein network diverges from those of other eukaryotes. Nature 2005, 438:108-112. 10.1038/ nature04135 16267557
32. Zhou XJ, Gibson G: Cross-species Comparison of Genome-wide Expression Patterns. Genome Biology 2004, 5(7):232. 463279 15239823 10.1186/ gb-2004-5-7-232
33. Yan X, Mehan M, Huang Y, Waterman MS, Yu PS, Zhou XJ: A Graph-based Approach to Systematically Reconstruct Human Transcriptional Regulatory Modules. Bioinformatics 2007, 23(13):i577 i586. 10.1093/bioinformatics/ btm227 17646346
34. SAlomi T, Segal D, Ruppin E, Sharan R: QPath: a method for querying pathways in a protein-protein interaction network. BMC bioinformatics 2006, 7:199. 1458361 16606460 10.1186/1471-2105-7-199
35. Ferro A, Giugno R, Pigolal G, Pulvirenti A, Skripin D, Bader GD, Shasha D: NAtMatch: a Cytoscape plugin for searching biological networks. Bioinformatics 2007, 23:910-912. 10.1093/bioinformatics/btm032 17277332
36. Durbin R Eddy SR Krogh A Mitchison GJ BiologicalSequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Cambridge: Cambridge University Press 1999.
37. He H, Singh AK: Closure-Tree: An Index Structure for Graph Queries Proceedings of the 22nd International Conference on Data Engineering (ICDE), Atlanta 2006, 38.
38. Medina M Genomes, phylogeny, and evolutionary systems biology Proc Natl Acad Sci USA 2005 102 6630 6635 1131869 15851668 10.1073/pnas.0501984102