Discovery and expansion of gene modules by seeking isolated groups in a random graph process

PLoS ONE

Volumn 3, Issue 10, 2008, Pages

  Brumm, Jochen ^a,b   Conibear, Elizabeth ^a,b   Wasserman, Wyeth W ^a,b   Bryan, Jennifer ^a,c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA DAMAGE; FUNGAL GENETICS; FUNGUS MUTANT; GENE INTERACTION; GENE ISOLATION; GENETIC ANALYSIS; NONHUMAN; PHENOTYPE; PREDICTION; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SURVIVAL TIME; SYSTEMS BIOLOGY; YEAST; ALGORITHM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPUTER SIMULATION; CYTOPLASM VESICLE; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; RANDOMIZATION; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER SIMULATION; CYTOPLASMIC VESICLES; DNA DAMAGE; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; PHENOTYPE; RANDOM ALLOCATION; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY; SYSTEMS BIOLOGY;

EID: 54449088033     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003358     Document Type: Article

References (23)

1. Beyer A, Bandyopadhyay S, Ideker T (2007) Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet 8:. 699-710.
2. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
3. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450.
4. Kiemer L, Costa S, Ueffing M, Cesareni G (2007) WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics 7: 932-943.
5. Rinner O, Mueller LN, Hubalek M, Muller M, Gstaiger M, et al. (2007) An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol 25: 345-352.
6. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
7. Hartuv E, Schmitt AO, Lange J, Meier-Ewert S, Lehrach H, et al. (2000) An algorithm for clustering cDNA fingerprints. Genomics 66: 249-256.
8. van Dongen S (2000) Graph clustering by flow simulation [PhD thesis]. Utrecht: University of Utrecht.
9. Ling RF (1973) A probability theory of cluster analysis. Journal of the American Statistical Association 68: 159-164.
10. Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, et al. (2005) Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet 1: e24.
11. Schluter C, Lam KK, Brumm J, Wu BW, Saunders M, et al. (2008) Global Analysis of Yeast Endosomal Transport Identifies the Vps55/68 Sorting Complex. Mol Biol Cell 19: 1282-1294.
12. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
13. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
14. Giaever G, Chu AM, Ni L, Connelly G, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
15. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
16. Brohee S, van Helden J (2006) Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7: 488.
17. Tibshirani K, Walther G, Hastie T (2001) Estimating the number of clusters in a data set via the gap statistic. Journal of the Royal Statistical Society, Series B 63: 411-423.
18. Milligan G, Cooper M (1985) An examination of procedures for determining the number of clusters in a data set. Psychometrika 50: 159-179.
19. Duda RO, Hart PE, Stork DG (2000) Pattern classification. New York; Chichester. John Wiley & Sons. 654 p.
20. Huber W, Carey VJ, Long L, Falcon S, Gentleman R (2007) Graphs in molecular biology. BMC Bioinformatics 8 Suppl 6: S8.
21. Stuetzle W (2003) Estimating the cluster tree of a density by analyzing the minimal spanning tree of a sample. Journal of Classification 20: 25-47.
22. Stuetzle W, Nugent R (2007) A generalized single linkage method for estimating the cluster tree of a density. University of Washington, Department of Statistics: Technical Report 514.
23. Wong MA, Lane T (1983) A kth Nearest Neighbour Clustering Procedure. Journal of the Royal Statistical Society Series B (Methodological) 45: 362-368.