Robust detection of hierarchical communities from escherichia coli gene expression data

PLoS Computational Biology

Volumn 8, Issue 2, 2012, Pages

  Treviño III, Santiago ^a,b   Sun, Yudong ^a,b   Cooper, Tim F ^a   Bassler, Kevin E ^a,b  

^a University of Houston   (United States)

^b UNIVERSITY OF HOUSTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; GENE ONTOLOGY;

ALGORITHMICS; BIOLOGICAL NETWORKS; FUNCTIONAL STRUCTURE; GENE EXPRESSION DATA; GENE INTERACTIONS; HIERARCHICAL COMMUNITIES; INFERRED NETWORKS; ROBUST DETECTION; STOCHASTICITY; SYSTEMS BIOLOGY;

ESCHERICHIA COLI;

ALGORITHM; ARTICLE; BACTERIAL GENE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE INACTIVATION; GENE INTERACTION; GENE LOCATION; GENE REGULATORY NETWORK; GENETIC DATABASE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; NONHUMAN; PREDICTION; SIGNAL NOISE RATIO; SPECIES DISTRIBUTION; BIOLOGICAL MODEL; BIOLOGY; DNA MICROARRAY; FLAGELLUM; GENE EXPRESSION; GENETICS; METABOLISM; METHODOLOGY; STATISTICAL MODEL; SYSTEMS BIOLOGY;

ESCHERICHIA COLI;

ESCHERICHIA COLI PROTEIN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLAGELLA; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SYSTEMS BIOLOGY;

EID: 84861180215     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002391     Document Type: Article

References (61)

1. Balázsi G, Heath AP, Shi L, Gennaro ML, (2008) The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol Sys Biol 4: 225.
2. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, et al. (2002) A genomic regulatory network for development. Science 295: 1669-1678.
3. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8.
4. Ma HW, Buer J, Zeng AP, (2004) Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 5: 199.
5. Cooper TF, Remold SK, Lenski RE, Schneider D, (2008) Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli. PLoS Genetics 4: e35.
6. Shi Z, Derrow C, Zhang B, (2010) Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Sys Biol 4: 74.
7. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
8. Bonnet E, Tatari M, Michoel A, Marchal K, Berx G, et al. (2010) Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One 5: e10162.
9. Beyer A, Workman C, Hollunder J, Radke D, Moller U, et al. (2006) Integrated assessment and predication of transcription factor binding. PLoS Comp Biol 2: e70.
10. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
11. Barabási AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101.
12. Friedman N, Linial M, Pe'er D, Nachman I, (2000) Using bayesian networks to analyze expression data. J Comp Biol 7: 601.
13. Friedman N, (2004) Inferring cellular networks using probabilistic graphical models. Science 303: 799-805.
14. Gardner TS, Bernardo D, Lorenz D, Mendes P, (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
15. Veiga DFT, Dutta B, Balázsi G, (2010) Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol BioSys 6: 469-480.
16. Getz G, Levine E, Domany E, (2000) Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad Sci U S A 97: 12079-12084.
17. Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A 107: 6286-6291.
18. Fortunato S, (2010) Community detection in graphs. Phys Rep 486: 75-174.
19. Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, et al. (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A 95: 334.
20. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863.
21. Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ, et al. (1997) An information-intensive approach to the molecular pharmacology of cancer. Science 275: 343.
22. Seidman SB, (1983) Network structure and minimum degree. Soc Networks 5: 269-287.
23. Seidman SB, Foster BL, (1978) A graph theoretic generalization of the clique concept. J Math Sociol 6: 139-154.
24. Palla G, Derényi I, Farkas I, Vicsek T, (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814-818.
25. Palla G, Barabási AL, Vicsek T, (2007) Quantifying social group evolution. Nature 446: 664-667.
26. Luo F, Li B, Wan XF, Scheuermann R, (2009) Core and periphery structures in protein interaction networks. BMC Bioinformatics 10: S8.
27. Borgatii SP, Everett MG, (1999) Models of core/periphery structures. Soc Networks 21: 375-395.
28. Borgatii SP, Everett MG, (1999) Peripheries of cohesive subsets. Soc Networks 21: 397-407.
29. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM, (1999) Systematic determination of genetic network architecture. Nat Genet 22: 281.
30. Raychaudhuri S, Stuart JM, Altman RB, (2000) Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 2000: 455-456.
31. Alter O, Brown P, Botstein D, (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97: 10101.
32. Raghavan UN, Albert R, Kumara S, (2007) Near linear time algorithm to detect community structures in large-scale networks. Phys Rev E 76: 036106.
33. Lu Q, Korniss G, Szymanski B, (2009) The naming game in social networks: community formation and consensus engineering. Journal of Economic Interaction and Coordination 4: 221-235.
34. Blatt M, Wiseman S, Domany E, (1996) Superparamagnetic clustering of data. Phys Rev Lett 76: 3251-3254.
35. Reichardt J, Bornholdt S, (2004) Detecting fuzzy community structures in complex networks with a potts model. Phys Rev Lett 93: 218701.
36. Newman MEJ, Girvan M, (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
37. Newman MEJ, (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103: 8577-8582.
38. Guimerà R, Sales-Pardo M, Amaral LAN, (2004) Modularity from fluctuations in random graphs and complex networks. Phys Rev E 70: 025101.
39. Duch J, Arenas A, (2005) Community detection in complex networks using extremal optimization. Phys Rev E 72: 027104.
40. Sun Y, Danila B, Josić K, Bassler KE, (2009) Improved community structure detection using a modified fine-tuning strategy. EPL (Europhysics Letters) 86: 28004.
41. Good BH, de Montijoyve YA, Clauset A, (2010) Performance of modularity maximization in practical contexts. Phys Rev E 81: 046106.
42. Chen J, Hsueh HM, Delongchamp R, Lin CJ, Tsa CA, (2007) Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 8: 412.
43. Baggerly K, Coombes K, Neeley E, (2008) Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncology 26: 1186-1187.
44. Duewer D, Jones W, Reid L, Salit M, (2009) Learning from microarray interlaboratory studies: measures of precision for gene expression. BMC Genet 10: 153.
45. Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, et al. (2008) Many microbe microarrays database: uniformly normalized affymetrix compendia with structured experimental metadata. Nucleic Acids Res 36: D866.
46. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muiz-Rascado L, et al. (2010) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (gensor units). Nucleic Acids Res 39: D98-105.
47. Kernighan BW, Lin S, (1970) An efficient heuristic procedure for partitioning graphs. Bell Systems Technical Journal 49: 291.
48. GO-Consortium (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29.
49. Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, et al. (2002) The EcoCyc database. Nucleic Acids Res 28: 56-58.
50. Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, et al. (2009) Implementation of genepattern within the stanford microarray database. Nucleic Acids Res 37 (Database Issue): D898-901.
51. Fortunato S, Barthélemy M, (2007) Resolution limit in community detection. Proc Natl Acad Sci U S A 104: 36-41.
52. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, et al. (2006) Escherichia coli k-12: a cooperatively developed annotation snapshot2005. Nucleic Acids Res 34: 1-9.
53. Barker MM, Gaal T, Josaitis CA, Gourse RL, (2001) Mechanism of regulation of transcription initiation by ppGpp. i. effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 305: 673-688.
54. Lemke J, Sanchez-Vazquez P, Burgos H, Hedberg G, Ross W, et al. (2011) Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DskA. Proc Natl Acad Sci U S A 108: 5712-5717.
55. Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, et al. (2008) The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 68: 1128-1148.
56. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, et al. (2005) Multiple-laboratory comparison of microarray platforms. Nat Meth 2: 345-349.
57. Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A, (2009) Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. Science 297: 39.
58. Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, et al. (2011) Construction of regulatory networks using expression time-series data of a genotyped population. Proc Natl Acad Sci U S A 108: 19436-19441.
59. Daub CO, Steuer R, Selbig J, Kloska S, (2004) Estimating mutual information using B-spline functions- an improved similarity measure for analyzing gene expression data. BMC Bioinformatics 5: 118.
60. Brandes U, Delling D, Gaertler M, Goerke R, Hoefer M, et al. (2008) On modularity clustering. IEEE Trans Knowl Data Eng 20: 172.
61. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B (Methodological) 57: 289-300.