A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification

Computational Biology and Chemistry

Volumn 35, Issue 5, 2011, Pages 298-307

  Yu, Liang ^a   Gao, Lin ^a   Li, Kui ^a   Zhao, Yi ^b   Chiu, David K Y ^c  

^a XIDIAN UNIVERSITY   (China)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c UNIVERSITY OF GUELPH   (Canada)

Author keywords

Complexes; Degree distribution; Hierarchical agglomerative algorithm; Protein protein interaction (PPI) networks

Indexed keywords

AGGLOMERATIVE ALGORITHM; BIOLOGICAL CHARACTERISTIC; BIOLOGICAL SIGNIFICANCE; COMPLEXES; DEGREE DISTRIBUTIONS; FUNCTIONAL MODULES; GOLD STANDARDS; HIERARCHICAL AGGLOMERATIVE CLUSTERING ALGORITHM; HIERARCHICAL STRUCTURES; PROTEIN COMPLEXES; PROTEIN-PROTEIN INTERACTION NETWORKS; QUANTITATIVE MEASURES; SUBGRAPHS;

COMPLEXATION; GOLD COMPOUNDS; PROTEINS;

CLUSTERING ALGORITHMS;

MULTIPROTEIN COMPLEX; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; STATISTICS;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, BIOLOGICAL; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 80052132043     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2011.07.005     Document Type: Article

References (46)

1. B. Adamcsek, G. Palla, I.J. Farkas, I. Derenyi, and T. Vicsek CFinder: locating cliques and overlapping modules in biological networks Bioinformatics 22 2006 1021 1023
2. V. Arnau, S. Mars, and I. Marin Iterative cluster analysis of protein interaction data Bioinformatics 21 3 2005 364 378 (Pubitemid 40246608)
3. S. Asur, D. Ucar, and S. Parthasarathy An ensemble framework for clustering protein-protein interaction networks Bioinformatics 23 13 2007 i29 i40
4. G.D. Bader, and C.W.V. Hogue An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 4 2003 2
5. A.L. Barabasi, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nature Reviews Genetics 5 2 2004 101 113 (Pubitemid 38160277)
6. E. Boyle, S. Weng, H. Jin, D. Botstein, J. Cherry, and G. Sherlock GO: TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 20 2004 321 330
7. J. Chen, and B. Yuan Detecting functional modules in the yeast protein-protein interaction network Bioinformatics 22 2006 2283 2290 (Pubitemid 44390885)
8. H.N. Chua, W.K. Sung, and L. Wong Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions Bioinformatics 22 13 2006 1623 1630 (Pubitemid 43985296)
9. S.S. Dwight, M.A. Harris, K. Dolinski, C.A. Ball, G. Binkley, K.R. Christie, D.G. Fisk, L. Issel-Tarver, M. Schroeder, G. Sherlock, A. Sethuraman, S. Weng, D. Botstein, and J.M. Cherry Saccharomyces genome database provides secondary gene annotation using the gene ontology Nucleic Acids Research 30 2002 69 72 (Pubitemid 34679507)
10. A.J. Enright, S.V. Dongen, and C.A. Ouzounis An efficient algorithm for large-scale detection of protein families Nucleic Acids Research 30 7 2002 1575 1584 (Pubitemid 34679732)
11. I. Farkas, ÁbelD, G. Palla, and T. Vicsek Weighted network modules New Journal of Physics 9 2007 180
12. C.C. Friedel, J. Krumsiek, and R. Zimmer Bootstrapping the interactome: unsupervised identification of protein complexes in yeast Journal of Computational Biology 16 8 2009 1 17
13. A.C. Gavin, M. Bösche, and R. Krause Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147 (Pubitemid 34059510)
14. A.C. Gavin, P. Aloy, and P. Grandi Proteome survey reveals modularity of the yeast cell machinery Nature 440 7084 2006 631 636
15. H. Ge UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions Nucleic Acids Research 28 2 2000 e3
16. A.C. Gingras, R. Aebersold, and B. Raught Advances in protein complex analysis using mass spectrometry Journal of Physiology 563 2005 11 21 (Pubitemid 40340364)
17. L. Giot, J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, B. Godwin, and E. Vitols A protein interaction map of Drosophila melanogaster Science 302 2004 1727 1736
18. U. Güldener, M. Münsterkötter, and G. Kastenmüller CYGD: the comprehensive yeast genome database Nucleic Acids Research 33 Database issue 2005 D364 D368
19. M. Habibi, C. Eslahchi, and L. Wong Protein complex prediction based on k-connected subgraphs in protein interaction network BMC Systems Biology 4 2010 129
20. L.H. Hartwell, J.J. Hopfield, S. Leibler, and A.W. Murray From molecular to modular cell biology Nature 402 1999 C47 C52
21. Y. Ho, A. Gruhler, and A. Heilbut Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180 183 (Pubitemid 34059520)
22. T. Ito, K. Tashiro, S. Muta, R. Ozawa, T. Chiba, M. Nishizawa, K. Yamamoto, S. Kuhara, and Y. Sakaki Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins Proceedings of the National Academy of Sciences of The United States of America 97 2000 1143 1147 (Pubitemid 30080826)
23. A.D. King, N. Przulj, and I. Jurisica Protein complex prediction via cost-based clustering Bioinformatics 20 17 2004 3013 3020 (Pubitemid 39619193)
24. N.J. Krogan, W.T. Peng, and G. Cagney High-definition macromolecular composition of yeast RNA-processing complexes Molecular Cell 13 2004 225 239 (Pubitemid 38183269)
25. N.J. Krogan, G. Cagney, and H. Yu Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440 7084 2006 637 643
26. H.C. Leung, Q. Xiang, S.M. Yiu, and F.Y. Chin Predicting protein complexes from PPI data: a core-attachment approach Journal of Computational Biology 16 2 2009 133 144
27. H. Liu, Y. Chiang, J. Pan, J. Chen, C. Salvadore, D. Audino, V. Badarinarayana, V. Palaniswamy, B. Anderson, and C. DenisDagger Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme JBC 276 10 2001 7541 7548
28. L.M. Markillie, C.T. Lin, J.N. Adkins, D.L. Auberry, E.A. Hill, B.S. Hooker, P.A. Moore, R.J. Moore, L. Shi, H.S. Wiley, and V. Kery Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks Journal of Proteome Research 4 2005 268 274 (Pubitemid 40548131)
29. J.B. Pereira-Leal, A.J. Enright, and C.A. Ouzounis Detection of functional modules from protein interaction networks Proteins 54 2004 49 57 (Pubitemid 38036914)
30. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Parisi Defining and identifying communities in networks Proceedings of the National Academy of Sciences of The United States of America 101 2004 2658 2663 (Pubitemid 38327665)
31. E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabási Hierarchical organization of modularity in metabolic networks Science 297 5586 2002 1551 1555 (Pubitemid 34971002)
32. A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munsterkotter, and H.W. Mewes The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Nucleic Acids Research 32 2004 5539 5545 (Pubitemid 39545671)
33. R. Saito, H. Suzuki, and Y. Hayashizaki Interaction generality, a measurement to assess the reliability of a protein-protein interaction Nucleic Acids Research 30 5 2002 1163 1168 (Pubitemid 34679688)
34. R. Saito, H. Suzuki, and Y. Hayashizaki Construction of reliable protein-protein interaction networks with a new interaction generality measure Bioinformatics 19 6 2003 756 763 (Pubitemid 36511900)
35. D.F. Seals, G. Eitzen, N. Margolis, W.T. Wickner, and A. Price A ypt/rab effector complex containing the sec1 homolog vps33p is required for homotypic vacuole fusion Proceedings of the National Academy of Sciences 97 17 2000 9402 9407 (Pubitemid 30650787)
36. V. Spirin, and L.A. Mirny Protein complexes and functional modules in molecular networks Proceedings of the National Academy of Sciences of The United States of America 100 21 2003 12123 12128 (Pubitemid 37271525)
37. A. Tanay, R. Sharan, M. Kupiec, and R. Shamir Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data Proceedings of the National Academy of Sciences 101 9 2004 2981 2986 (Pubitemid 38327722)
38. A.H. Tong, B. Drees, G. Nardelli, G.D. Bader, B. Brannetti, and L. Castagnoli A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules Science 295 2002 321 324 (Pubitemid 34074361)
39. D. Ucar, S. Parthasarathy, S. Asur, and C. Wang Effective pre-processing strategies for functional clustering of a protein-protein interactions network Proceedings of the IEEE 5th Symposium on Bioinformatics & Bioengineering (BIBE05), October 2005 2005
40. D. Ucar, S. Asur, U. Catalyurek, and S. Parthasarathy Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-Induced Subgraphs 2006 PKDD
41. C. von Mering, R. Krause, B. Snel, M. Cornell, S. Oliver, S. Fields, and P. Bork Comparative assessment of large-scale data sets of protein-protein interactions Nature 417 6887 2002 399 403 (Pubitemid 34563526)
42. L.F. Wu, T.R. Hughes, A.P. Davierwala, M.D. Robinson, R. Stoughton, and S.J. Altschuler Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters Nature Genetics 31 2002 255 265
43. M. Wu, X. Li, C.K. Kwoh, and S.K. Ng A core-attachment based method to detect protein complexes in PPI networks BMC Bioinformatics 10 2009 169
44. S.H. Yook, Z.N. Oltvai, and A.L. Barabsi Functional and topological characterization of protein interaction networks Proteomics 4 4 2004 928 942 (Pubitemid 38445953)
45. S. Zhang, X. Ning, and X.S. Zhang Identification of functional modules in a PPI network by clique percolation clustering Computational Biology and Chemistry 30 6 2006 445 451 (Pubitemid 44792556)
46. H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R.A. Dean, M. Gerstein, and M. Snyder Global analysis of protein activities using proteome chips Science 293 5537 2001 2101 2105 (Pubitemid 32848060)