Identifying responsive functional modules from protein-protein interaction network

Molecules and Cells

Volumn 27, Issue 3, 2009, Pages 271-277

  Wu, Zikai ^a   Zhao, Xingming ^a   Chen, Luonan ^a  

^a SHANGHAI UNIVERSITY   (China)

Author keywords

Optimization; Protein protein interaction network; Responsive functional module; Signaling pathway; Systems biology

Indexed keywords

MEMBRANE PROTEIN; TRANSCRIPTION FACTOR; PROTEIN;

ALGORITHM; BIOINFORMATICS; GENE EXPRESSION; GENOMICS; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SHORT SURVEY; SIGNAL NOISE RATIO; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; BIOLOGICAL MODEL; COMPUTER SIMULATION; HUMAN; METABOLISM; PROTEIN ANALYSIS; PROTEIN MICROARRAY; REVIEW;

COMPUTER SIMULATION; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 70349331032     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10059-009-0035-x     Document Type: Short Survey

References (62)

1. B. Adamcsek G. Palla I. Farkas I. Derényi T. Vicsek 2006 Cfinder: locating cliques and overlapping modules in biological networks Bioinformatics 22 1021 1023 16473872 10.1093/bioinformatics/btl039 1:CAS:528: DC%2BD28XjtFSktbc%3D
2. R. Albert B. DasGupta R. Dondi S. Kachalo E. Sontag A. Zelikovsky K. Westbrooks 2007 A novel method for signal transduction network inference from indirect experimental evidence J. Comput. Biol. 14 927 949 17803371 10.1089/cmb.2007.0015 1:CAS:528:DC%2BD2sXpvFWhs7w%3D (Pubitemid 47427600)
3. N. Alon R. Yuster U. Zwick 1995 Color-coding J. ACM. 42 844 856 10.1145/210332.210337
4. K. Arga Z. Önsan B. Kiidar K. Ölgen J. Nielsen 2007 Understanding signaling in yeast: insights from network analysis Biotechnol. Bioeng. 97 1246 1258 17252576 10.1002/bit.21317 1:CAS:528:DC%2BD2sXnvFagt7o%3D (Pubitemid 47195320)
5. C. Backes A. Keller J. Kuentzer B. Kneissl N. Comtesse Y. Elnakady R. Müller E. Meese H. Lenhof 2007 Gene Trail-advanced gene set enrichment analysis Nucleic Acids Res. 35 W186 W192 17526521 10.1093/nar/gkm323
6. G. Bader C. Hogue 2003 An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 4 2 12525261 10.1186/1471-2105-4-2 (Pubitemid 38751268)
7. A.L. Barabási Z.N. OltVai 2004 Network biology: understanding the cell's functional organization Nat. Rev. Genet. 5 101 113 14735121 10.1038/nrg1272 (Pubitemid 38160277)
8. G. Bebek J. Yang 2007 Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks BMC Bioinformatics 8 335 17854489 10.1186/1471-2105-8-335 (Pubitemid 350226857)
9. Bild, A., and Febbo, P. (2005). Application of a priori established gene sets to discover biologically important differential expression in microarray data. Proc. Natl. Acad. Sci. USA 102, 15278-15279.
10. L. Cabusora E. Sutton A. Fulmer C. Forst 2005 Differential network expression during drug and stress response Biofinromatics 21 2898 2905 10.1093/bioinformatics/bti440 1:CAS:528:DC%2BD2MXlvFSrtb8%3D (Pubitemid 40862290)
11. X. Chen L. Wang J. Smith P. Zhang 2008 Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes Bioinformatics 24 2474 2481 18753155 10.1093/bioinformatics/btn458 1:CAS:528:DC%2BD1cXht12gtbvK
12. Chen, L., Wang, R., and Zhang, X.S. (2009). Biomolecular networks: methods and applications in systems biology (New Jersey, USA: Wiley Interscience).
13. Y. Cho W. Hwang M. Ramanathan A. Zhang 2007 Semantic integration to identify overlapping functional modules in protein interaction networks BMC Bioinformatics 8 265 17650343 10.1186/1471-2105-8-265 (Pubitemid 47377005)
14. W. Chu Z. Ghahramani 2006 Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model Pacific Symposium on Biocomputing 11 231 242 10.1142/9789812701626-0022
15. H. Chu B. Chen 2008 Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets BMC Syst. Biol. 2 56 18590547 10.1186/1752-0509-2-56
16. H. Chuang E. Lee Y. Liu D. Lee T. Ideker 2007 Network-based classification of breast cancer metastasis Mol. Syst. Biol. 3 140 17940530 10.1038/msb4100180 (Pubitemid 47587026)
17. M. Dittrich G. Klau A. Rosenwald T. Dandekarand T. Muller 2008 Identifying functional modules in protein-protein interaction networks: an integrated exact approach Bioinformatics 24 i223 i231 18586718 10.1093/bioinformatics/btn161 1:CAS:528:DC%2BD1cXnvV2rtrk%3D (Pubitemid 351911677)
18. Z. Guo Y. Li X. Gong C. Yao W. Ma D. Wang Y. Li J. Zhu M. Zhang D. Yang, et al. 2007 Edge-based scoring and searching method for identifying condition-responsive proteinprotein interaction sub-network Bioinformatics 23 2121 2128 17545181 10.1093/bioinformatics/btm294 1:CAS:528:DC%2BD2sXhtVWqtrrO (Pubitemid 47394112)
19. J. Han N. Bertin T. Hao D. Goldberg G. Berriz L. Zhang D. Dupuy A. Walhout M. Cusick F. Roth, et al. 2004 Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 430 88 93 15190252 10.1038/nature02555 1:CAS:528:DC%2BD2cXlt1Cqt7s%3D (Pubitemid 38915230)
20. E. Hirsh R. Sharan 2006 Identification of conserved protein complexes based on a model of protein network evolution Bioinformatics 23 e170 e176 10.1093/bioinformatics/btl295
21. M. Holden S. Deng L. Wojnowski B. Kulle 2008 GSEASNP: applying gene set enrichment analysis to SNP data from genome-wide association studies Bioinformatics 24 2784 2785 18854360 10.1093/bioinformatics/btn516 1:CAS:528:DC%2BD1cXhsVWmsrfL (Pubitemid 352722627)
22. R. Huang A. Wallqvist D. Covell 2006 Targeting changes in cancer: assessing pathway stability by comparing pathway gene expression coherence levels in tumor and normal tissues Mol. Cancer Ther. 5 2417 2427 16985076 10.1158/1535-7163.MCT-06-0239 1:CAS:528:DC%2BD28Xps1ynsbY%3D (Pubitemid 44530479)
23. W. Hwang Y. Cho A. Zhang M. Ramanathan 2006 A novel functional module detection algorithm for protein-protein interaction networks Algorithms Mol. Biol. 1 24 17147822 10.1186/1748-7188-1-24 (Pubitemid 46736696)
24. T. Ideker R. Sharan 2008 Protein networks in disease Genome Res. 18 644 652 18381899 10.1101/gr.071852.107 1:CAS:528:DC%2BD1cXks1alsb8%3D
25. T. Ideker O. Ozier B. schwikowski A. Siegel 2002 Discovering regulatory and signalling circuits in molecular interaction networks Bioinformatics 18 S233 S240 12169552
26. R. Jansen D. Greenbaum M. Gerstein 2002 Relating whole-genome expression data with protein-protein interactions Genome Res. 12 37 46 11779829 10.1101/gr.205602 1:CAS:528:DC%2BD38XksV2rtw%3D%3D (Pubitemid 34065588)
27. M. Kann 2007 Protein interactions and disease: computational approaches to uncover the etiology of diseases Brief. Bioinform. 8 333 346 17638813 10.1093/bib/bbm031 1:CAS:528:DC%2BD2sXhsVGgtr%2FN (Pubitemid 350142622)
28. A. King N. Pržulj I. Jurisica 2004 Protein complex prediction via cost-based clustering Bioinformatics 20 3013 3020 15180928 10.1093/ bioinformatics/bth351 1:CAS:528:DC%2BD2cXhtVSrur%2FI (Pubitemid 39619193)
29. S. Li S. Assmann R. Albert 2006 Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling PLoS Biol. 4 e312 16968132 10.1371/journal.pbio.0040312 (Pubitemid 44610093)
30. Y. Liu H. Zhao 2004 A computational approach for ordering signal transduction pathway components from genomics and proteomics data BMC Bioinformatics 5 158 15504238 10.1186/1471-2105-5-158 (Pubitemid 40195350)
31. M. Liu A. Liberzon S. Kong W. Lai P. Park I. Kohane S. Kasif 2007 Network-based analysis of affected biological processes in type 2 diabetes models PLOS Genet. 3 e96 17571924 10.1371/journal.pgen.0030096 (Pubitemid 47015856)
32. M. Mete F. Tang X. Xu N. Yuruk 2008 A structural approach for finding functional modules from large biological networks BMC Bioinformatics 9 S19 18793464 10.1186/1471-2105-9-S9-S19
33. T. Murali C. Rivera 2008 Network legos: buiding blocks of cellular wiring diagrams J. Comput. Biol. 15 829 844 18707557 10.1089/cmb.2007.0139 1:CAS:528:DC%2BD1cXhtVOmurbO
34. S. Nacu R. Critchley-Thorne P. Lee S. Holmes 2007 Gene expression network analysis and applications to immunology Bioinformatics 23 850 858 17267429 10.1093/bioinformatics/btm019 1:CAS:528:DC%2BD2sXmtVOjurw%3D (Pubitemid 47049919)
35. D. Nettleton J. Recknor J. Reecy 2008 Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis Bioinformatics 24 192 201 18042553 10.1093/bioinformatics/btm583 1:CAS:528:DC%2BD1cXptlWhsA%3D%3D
36. J. Noisel G. Sanguinetti P. Wright 2008 Identifying differentially- expressed subnetworks with MMG Bioinformatics 24 2792 2793 10.1093/ bioinformatics/btn499 (Pubitemid 352722631)
37. A. Oron Z. Jiang R. Gentleman 2008 Gene set enrichment analysis using linear models and diagnostics Bioinformatics 24 2586 2591 18790795 10.1093/bioinformatics/btn465 1:CAS:528:DC%2BD1cXhtlGht7%2FN
38. J. Pereira-Leal A. Enright C. Ouzounis 2004 Detection of functional modules from protein interaction networks Proteins 54 49 57 14705023 10.1002/prot.10505 1:CAS:528:DC%2BD2cXlsFSitA%3D%3D (Pubitemid 38036914)
39. Y. Qi F. Balem C. Faloutsos J. Klein-Seetharaman Z. Bar-Joseph 2008 Protein complex identification by supervised graph local clustering Bioinformatics 24 i250 i258 18586722 10.1093/bioinformatics/btn164 1:CAS:528:DC%2BD1cXnvV2rtrY%3D (Pubitemid 351911680)
40. Y. Qiu S. Zhang 2008 Uncovering Differentially expressed Pathways with protein Interation and gene expression data Lecture Notes in Operations Res. 9 74 82
41. Qiu, Y., Zhang, S., Zhang, X-S., and Chen, L. (2009). Identifying differentially expressed pathways by high throughput data. IET Syst. Biol. (in press).
42. Rahnenfuhrer, J., Domingues, F., Maydt, J., and Lengauer, T. (2004). Calculating the statistical significance of changes in pathway activity from gene expression data. Stat. Appl. Gen. Mol. Biol. 3, Article 16.
43. D. Rajagopalan P. Agarwal 2005 Inferring pathways from gene lists using a literature-derived network of biological relationships Bioinformatics 21 788 793 15509611 10.1093/bioinformatics/bti069 1:CAS:528:DC%2BD2MXit1Kntrc%3D (Pubitemid 40439415)
44. D. Scholtens M. Vidal R. Gentleman 2005 Local modeling of global interactome networks Bioinformatics 21 3548 3557 15998662 10.1093/ bioinformatics/bti567 1:CAS:528:DC%2BD2MXpsValsr0%3D (Pubitemid 41236000)
45. M. Scott T. Perkins S. Bunnell F. Pepin D. Thomas M. Hallett 2005 Identifying regulatory subnetworks for a set of genes Mol. Cell. Proteomics 4 683 692 15722371 10.1074/mcp.M400110-MCP200 1:CAS:528:DC%2BD2MXktlSms70%3D (Pubitemid 40862246)
46. J. Scott T. Ideker R. Karp R. Sharan 2006 Efficient algorithms for detecting signaling pathways in protein interaction networks J. Comput. Biol. 13 133 144 16597231 10.1089/cmb.2006.13.133 1:CAS:528:DC%2BD28XjtFKisrw%3D
47. R. Sharan T. Ideker B.P. Kelley R. Shamir R.M. Karp 2005 Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data J. Comput. Biol. 12 835 846 16108720 10.1089/cmb.2005.12.835 1:CAS:528:DC%2BD2MXotFemsLs%3D (Pubitemid 41170485)
48. F. Sohler D. Hanisch R. Zimmer 2004 New methods for joint analysis of biological networks and expression data Bioinformatics 20 1517 1521 15231545 10.1093/bioinformatics/bth112 1:CAS:528:DC%2BD2cXltlOqtLw%3D (Pubitemid 39023155)
49. V. Spirin L. Mirny 2003 Protein complexes and functional modules in molecular networks Proc. Natl Acad. Sci. USA 100 12123 12128 14517352 10.1073/pnas.2032324100 1:CAS:528:DC%2BD3sXotlGlurY%3D (Pubitemid 37271525)
50. M. Steffen A. Petti J. Aach P. D'haeseleer G. Church 2002 Automated modelling of signal transduction networks BMC Bioinformatics 3 34 12413400 10.1186/1471-2105-3-34 (Pubitemid 38751170)
51. A. Subramaniana P. Tamayo V. Mootha S. Mukherjee B. Ebert M. Gillette A. Paulovich S. Pomeroy T. Golub E. Lander, et al. 2005 Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 15545 15550 10.1073/pnas.0506580102 (Pubitemid 41528093)
52. M. Suderman H. Michael 2007 Tools for visually exploring biological networks Bioinformatics 23 2651 2659 17720984 10.1093/bioinformatics/btm401 1:CAS:528:DC%2BD2sXht1KmtLvL (Pubitemid 350048327)
53. M. Turanalp T. Can 2008 Discovering functional interaction patterns in protein-protein interaction networks BMC Bioinformatics 9 276 18547430 10.1186/1471-2105-9-276 (Pubitemid 351943948)
54. I. Ulitsky M. Karp R. Shamir 2008 Detecting diseasespecific dysregulated pathways via analysis of clinical expression profiles Lect. N. Bioinformat. (RECOMB2008) 4955 347 359
55. Y. Wang Y. Xia 2008 Condition specific subnetwork identification using an optimization model Lecture Notes in Operations Res. 9 333 340
56. R. Wang S. Zhang X. Zhang L. Chen 2006 Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks Lect. N. Bioinformat. 4682 1090 1101
57. D. Watts S. Atrogatz 1998 Collective dynamics of 'small word' networks Nature 393 440 442 9623998 10.1038/30918 1:CAS:528:DyaK1cXjs1Khsrk%3D (Pubitemid 28292183)
58. S. Zhang X. Ning X. Zhang 2006 Identification of functional modules in a PPI network by clique percolaion clusering Comput. Biol. Chem. 30 445 451 17098476 10.1016/j.compbiolchem.2006.10.001 1:CAS:528:DC%2BD28Xht1Kmtr7F (Pubitemid 44792556)
59. S. Zhang G. Jin X. Zhang L. Chen 2007 Discovering functions and revealing mechanisms at molecular level from biological networks Proteomics 7 2856 2869 17703505 10.1002/pmic.200700095 1:CAS:528:DC%2BD2sXhtVels7fL (Pubitemid 47359926)
60. Zhao, X., Wang, R., Chen, L., and Aihara, K. (2008a). Automatic modeling of signal pathways from protein-protein interaction networks. In A., Brazma, S., Miyano, and T., Akutsu, eds., Proceedings of The 6th Asia Pacific Bioinformatics Conference, Vol. 6 of Serias on advances in bioinformatics and computational biology Imperial College Press, Singapore, 287-296.
61. X. Zhao R. Wang L. Chen K. Aihara 2008 Uncovering signal transduction networks from high-throughput data by integer linear programming Nucleic Acids Res. 36 e48 18411207 10.1093/nar/gkn145 (Pubitemid 351737207)
62. Zhao, X., Wang, R., Chen, L., and Aihara, K. (2009). Automatic modeling of signaling pathways based on network flow model. J. Bioinformat. Computational Biol. (in press).