An agglomerate algorithm for mining overlapping and hierarchical functional modules in protein interaction networks

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6053 LNBI, Issue , 2010, Pages 140-151

  Ren, Jun ^a,b   Wang, Jianxin ^a   Chen, Jianâer ^a   Li, Min ^a   Chen, Gang ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b HUNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

agglomerative algorithm; hierarchical module structure; Overlapping functional module

Indexed keywords

AGGLOMERATIVE ALGORITHM; BIOLOGICAL SIGNIFICANCE; FUNCTIONAL MODULES; HIERARCHICAL MODULES; LARGE SIZES; P-VALUES; PROTEIN INTERACTION NETWORKS; SUBGRAPHS; TIME COMPLEXITY;

BIOINFORMATICS;

ALGORITHMS;

EID: 77953762415     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-13078-6_17     Document Type: Conference Paper

References (23)

1. Xenarios, I., Salwínski, L., et al.: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303-305 (2002)
2. Mewes, H.W., Frishman, D., Gruber, C., Geier, B., Haase, D., Kaps, A.: MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 28, 37-40 (2000)
3. Issel-Tarver, L., Christie, K.R., Dolinski, K., et al.: Saccharomyces Genome Database. Methods Enzymol. 350, 329-346 (2002)
4. Barabasi, A.L., Oltvai, Z.N.: Network biology: understanding the cell's functional organization. Nat. Res. 5, 101-114 (2004)
5. Chen, J.C., Yuan, B.: Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 22(18), 2283-2290 (2006)
6. Luo, F., Yang, Y., Chen, C.F., Chang, R., Zhou, J., Scheuermann, R.H.: Modular organization of protein interaction networks. Bioinformatics 23(2), 207-214 (2007)
7. Rives, A.W., Galitski, T.: Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA 100, 1128-1133 (2003)
8. Girvan, M., Newman, M.E.: Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA 99, 7821-7826 (2002)
9. Girvan, M., Newman, M.E.: Finding and evaluating community structure in networks. Phys. Rev. E 69(2), 026113 (2004)
10. Li, M., Wang, J.X., Chen, J.: A Fast Agglomerative algorithm for Mining Functional Modules in Protein Interaction Networks. In: BMEI 2008, pp. 3-7. IEEE press, Los Alamitos (2008)
11. Li, M., Wang, J.X., Chen, J.: Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. In: M?ndoiu, I., Narasimhan, G., Zhang, Y. (eds.) ISBRA 2009. LNBIP, vol.5542, pp. 75-86. Springer, Heidelberg (2009)
12. Radicchi, F., Castellano, C., Cecconi, F., Loreto, V., Parisi, D.: Defining and identifying communities in networks. Proc. Natl.Acad. Sci. USA 101, 2658-2663 (2004)
13. Palla, G., Dernyi, I., Farkas, I.J., Vicsek, T.: Uncoverring the overlapping community structure of complex networks in nature and society. Nature 435(7043), 814-818 (2005)
14. Adamcsek, B., Palla, G., Farkas, I.J., Derényi, I., Vicsek, T.: CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22(8), 1021-1023 (2006)
15. Bader, G.D., Hogue, C.: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003)
16. Altaf-UI-Amin, M., Shinbo, Y., Mihara, K., et al.: Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7, 207 (2006)
17. Shen, H., Cheng, X., Cai, K.: Detect overlapping and hierarchical community structure in networks. Physica A 388(8), 1706-1721 (2009)
18. Přulj, N., Wigle, D.A., Jurisica, I.: Functional topology in a network of protein interactions. Bioinformatics 20(3), 340-348 (2004)
19. Wuchty, S., Almaas, E.: Peeling the yeast protein network. Proteomics 5(2), 444-449 (2005)
20. Yook, S., Oltvai, Z., Barabási, A.: Functional and topological characterization of protein interaction networks. Proteomics 4, 928-942 (2004)
21. King, A.D., Przulj, N., Jurisica, I.: Protein complex prediction via cost-based clustering. Bioinformatics 20, 3013-3020 (2004)
22. Cho, Y.R., Hwang, W., Ramanathan, M., et al.: Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 8, 265 (2007)
23. Ashburner, M., Ball, C.A., Blake, J.A., et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25, 25-29 (2000)