Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: The existence of genome vehicles revealed

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Tsuchiya, Masa ^a   Piras, Vincent ^a   Giuliani, Alessandro ^b   Tomita, Masaru ^a   Selvarajoo, Kumar ^a  

^a KEIO UNIVERSITY   (Japan)

^b ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DIMETHYL SULFOXIDE; RETINOIC ACID;

ARTICLE; CELL DIFFERENTIATION; CELL FATE; CONTROLLED STUDY; GENE EXPRESSION; GENETIC CORRELATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME SIZE; HUMAN; HUMAN CELL; MOLECULAR DYNAMICS; NEUTROPHIL; PROBABILITY; CELL STRAIN HL 60; CYTOLOGY; DNA MICROARRAY; DRUG EFFECT; FRACTAL ANALYSIS; GENE EXPRESSION PROFILING; GENETICS; GENOME; GENOMICS; METABOLISM; METHODOLOGY;

ATRA;

CELL DIFFERENTIATION; DIMETHYL SULFOXIDE; FRACTALS; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HL-60 CELLS; HUMANS; NEUTROPHILS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROBABILITY; TRETINOIN;

EID: 77957881755     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012116     Document Type: Article

References (34)

1. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU (2006) Complex networks: Structure and dynamics. Physics Reports 424: 175-308.
2. Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genetics 5: 101-113.
3. Nadell CD, Xavier JB, Levin SA, Foster KR (2008) The Evolution of Quorum Sensing in Bacterial Biofilms. PLoS Biol 6: e14.
4. Danino T, Mondragón-Palomino O, Tsimring L, Hasty J (2010) A synchronized quorum of genetic clocks. Nature 463: 326-330.
5. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, et al. (2010) Visualization of omics data for systems biology. Nat Methods 7(Suppl 3): S56-68.
6. 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.
7. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. (2007) Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations. Science 316: 593-597.
8. Tsuchiya M, Wong ST, Yeo ZX, Colosimo A, Palumbo MC, et al. (2007) Gene expression waves. Cell cycle independent collective dynamics in cultured cells. FEBS J 274: 2878-2886.
9. Huang S, Eichler G, Bar-Yam Y, Ingber DE (2005) Cell fates as highdimensional attractor states of a complex gene regulatory network. Phys Rev Lett 94: 128701.
10. Waddington CH (1957) The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology. New York: Macmillan.
11. Kauffman SA (1969) Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets. J Theor Biol 22: 437-467.
12. Kauffman SA (1993) The Origins of Order. New York: Oxford University Press.
13. Huang S (2009) Reprogramming cell fates: reconciling rarity with robustness. Bioessays 31: 546-560.
14. Shchepinov MS, Case-Green SC, Southern EM (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res 25: 1155-1161.
15. Forman JE, Walton ID, Stern D, Rava RP, Trulson MO (1998) Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. In: Leontis NB, JohnSantaLucia, eds. Molecular Modeling of Nucleic Acids. Washington DC: American Chemical Society. pp 206-228.
16. Southern E, Mir K, Shchepinov M (1999) Molecular interactions on microarrays. Nat Genet 21: 5-9.
17. Tsuchiya M, Selvarajoo K, Piras V, Tomita M, Giuliani A (2009) Local and global responses in complex gene regulation networks. Physica A 388: 1738-1746.
18. Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, et al. (2009) Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides- Stimulated Macrophages. PLoS ONE 4: e4905.
19. Lee YR, Shim HJ, Yu HN, Song EK, Park J, et al. (2005) Dimethylsulfoxide induces upregulation of tumor suppressor protein PTEN through nuclear factorkB activation in HL-60 cells. Leuk Res 29: 401-405.
20. Klein ES, Wang JW, Khalifa B, Gavigan SA, Chandraratna RAS (2000) Recruitment of nuclear corepressor and coactivator to the retinoic acid receptor by retinoid ligands. J Biol Chem 275: 19401-19408.
21. Chang HH, Oh PY, Ingber DE, Huang S (2006) Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol 7: 11.
22. Farmer JD (1985) Sensitive dependence on parameters in nonlinear dynamics. Phys Rev Lett 55: 351-354.
23. Umberger DK, Farmer JD (1985) Fat fractals on the energy surface. Phys Rev Lett 55: 661-664.
24. Komarova N, Soffer A (2005) Nonlinear waves in double-stranded DNA. Bull Math Biol 67: 701-718.
25. Yakushevich LV (2007) Is DNA a nonlinear dynamical system where solitary conformational waves are possible? J Biosci 26: 305-313.
26. Takahashi K, Yamanaka S (2006) Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell 126: 663-676.
27. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, et al. (1998) The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
28. Chang H, Hemberg M, Barahona M, Ingber DE, Huang S (2008) Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453: 544-548.
29. Butte AJ, Kohane IS (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000: 418-429.
30. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, et al. (2001) Geneexpression profiles in hereditary breast cancer. N Engl J Med 344: 539-548.
31. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
32. Steuer R, Kurths J, Daub CO, Weise J, Selbig J (2002) The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18(Suppl 2): S231-240.
33. Steuer R, Daub CO, Selbig J, Kurths J (2004) Measuring Distances between Variables by Mutual Information. In: Baier D, Wernecke KD, eds. Innovations in Classification, Data Science, and Information Systems, Proceedings of the 27th Annual GfKl Conference. Springer Verlag. pp 81-90.
34. Venables WN, Ripley BD (2002) Modern Applied Statistics with S Springer Verlag.