Biological process linkage networks

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Dotan Cohen, Dikla ^a   Letovsky, Stan ^b,d   Melkman, Avraham A ^a   Kasif, Simon ^c,d,e  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b Codon Devices ^*  (United States)

^c Boston University   (United States)

^d BOSTON UNIVERSITY   (United States)

^e HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOLOGY; GENE EXPRESSION REGULATION; GENE INTERACTION; LINKAGE ANALYSIS; METHODOLOGY; PREDICTION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION REGULATION; ALGORITHM; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; CHEMISTRY; GENE REGULATORY NETWORK; METABOLISM; PROTEIN DATABASE; SACCHAROMYCES CEREVISIAE;

PROTEIN;

ALGORITHMS; BIOLOGICAL PROCESSES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE REGULATORY NETWORKS; PROTEIN INTERACTION MAPPING; PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 65349115975     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005313     Document Type: Article

References (40)

1. Battle A, Segal E, Koller D (2005) Probabilistic discovery of overlapping cellular processes and their regulation. J Comput Biol 12: 909-927.
2. Bork P, et al. (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14: 292-999.
3. Gavin AC, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 30: 631-636.
4. Huynen MA, Snel B, von Mering C, Bork P (2003) Function prediction and protein networks. Curr Opin Cell Biol 15: 191-198.
5. de Lichtenberg U, Jensen LJ, Brunak S, Bork P (2005) Dynamic complex formation during the yeast cell cycle. Science 307: 724-727.
6. Luo F, et al. (2006) Modular organization of protein interaction networks. Bioinformatics 23: 207-14.
7. Segal E, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
8. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
9. Lin D (1998) An information-theoretic definition of similarity. Proceedings of the 15th International Conference on Machine Learning. San Francisco, CA: Morgan Kaufmann. pp 296-304.
10. Unal E, Arbel-Eden A, Sattler U, Shroff R, et al. (2003) DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol Cell 16: 991-1002.
11. Larochelle M, Drouin S, Robert F, Turcotte B (2006) Oxidative stress-activated zinc cluster protein Stb5 has dual activator/repressor functions required for pentose phosphate pathway regulation and NADPH production. Mol Cell Biol 26: 6690-6701.
12. Spellman PT, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
13. Finley D, Bartel B, Varshavsky A (1989) The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Nature 30: 394-401.
14. Stavreva DA, et al. (2006) Potential Roles for Ubiquitin and the Proteasome during Ribosome Biogenesis. Mol Cell Biol 26: 5131-5145.
15. Sharan R, et al. (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A 102: 1974-1979.
16. Hishigaki H, et al. (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18: 523-531.
17. Hughes TR, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
18. Karaoz U, et al. (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A 101: 2888-2893.
19. Marcotte EM, et al. (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86.
20. Vazquez A, Flammini A, Maritan A, Vespignani A (2003) Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 21: 697-700.
21. Wu LF, et al. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet 31: 255-265.
22. Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18: 1257-1261.
23. Tong AH, et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321-324.
24. Wong SL, et al. (2004) Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A 101: 15682-15687.
25. Lu JL, Sboner A, Huang JY, Lu XH, Gianoulis AT, et al. (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends in Biochemical Sciences 32: 320-331.
26. Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566.
27. Segre D, Deluna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37: 77-83.
28. Guo X, et al. (2006) Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22: 967-973.
29. Lord PW, Stevens RD, Brass A, Goble CA (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283.
30. Lubovac Z, Gamalielsson J, Olsson B (2006) Combining functional and topological properties to identify core modules in protein interaction networks. Proteins 64: 948-959.
31. Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7: 302.
32. Xenarios I, et al. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
33. Harris MA, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
34. Giot L, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
35. Formstecher E, et al. (2005) Protein interaction mapping: a Drosophila case study. Genome Res 5: 376-384.
36. Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21: 2076-2082.
37. Butte AJ (2000) Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A 97: 12182-12186.
38. Stark C, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: 535-539.
39. Amaral LA, Scala A, Barthelemy M, Stanley HE (2000) Classes of small-world networks. Proc Natl Acad Sci U S A 97: 11149-11152.
40. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.