Empirical multiscale networks of cellular regulation

PLoS Computational Biology

Volumn 3, Issue 10, 2007, Pages 1968-1978

  De Bivort, Benjamin ^a   Huang, Sui ^b,c   Bar Yam, Yaneer ^d  

^a HARVARD UNIVERSITY   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d NEW ENGLAND COMPLEX SYSTEMS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE ONTOLOGY;

B LYMPHOCYTES; BIOLOGICAL FUNCTIONS; CELLS SIGNALING; CELLULAR CONDITIONS; CELLULAR ORGANIZATION; CELLULAR REGULATION; CELLULARS; CHEMOKINES; HIGH-THROUGHPUT APPROACHES; REGULATORY INTERACTIONS;

CELL SIGNALING;

ADENOSINE TRIPHOSPHATE; CHEMOKINE;

ARTICLE; B LYMPHOCYTE; BIOSYNTHESIS; CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL DISRUPTION; CELL FUNCTION; CELL INTERACTION; CELL PROLIFERATION; DNA REPLICATION; GENE FUNCTION; HUMAN; LYMPHOCYTE ACTIVATION; MEMBRANE STRUCTURE; MOLECULAR INTERACTION; NONHUMAN; REGULATORY MECHANISM;

MURINAE;

EID: 35748948951     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030207     Document Type: Article

References (36)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-C52.
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. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298: 824-827.
4. Oltvai ZN, Barabasi AL (2002) Systems biology. Life's complexity pyramid. Science 298: 763-764.
5. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
6. Simon HA (1996) Sciences of the artificial. Cambridge (Massachusetts): MIT Press. 231 p.
7. 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: 14863-14868.
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. Yanai I, DeLisi C (2002) The society of genes: Networks of functional links between genes from comparative genomics. Genome Biol 3: research0064.
10. Barabasi AL, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
11. D'Haeseleer P, Wen X, Fuhrman S, Somogyi R (1999) Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput 41-52.
12. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, et al. (2002) A genomic regulatory network for development. Science 295: 1669-1678.
13. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
14. Tegner J, Yeung MK, Hasty J, Collins JJ (2003) Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A 100: 5944-5949.
15. de Bivort B, Huang S, Bar-Yam Y (2004) Dynamics of cellular level function and regulation derived from murine expression array data. Proc Natl Acad Sci U S A 101: 17687-17692.
16. Bergmann S, Ihmels J, Barkai N (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2: E9. doi:10. 1371/journal.pbio.0020009
17. Ihmels J, Bergmann S, Berman J, Barkai N (2005) Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1: e39. doi:10.1371/journal.pgen.0010039
18. Ihmels J, Levy R, Barkai N (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92.
19. Voorma HO (1983) Regulatory steps in the initiation of protein synthesis. Horiz Biochem Biophys 7: 139-153.
20. Klevecz RR, Bolen J, Forrest G, Murray DB (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci U S A 101: 1200-1205.
21. Berger SL (1999) Gene activation by histone and factor acetyltransferases. Curr Opin Cell Biol 11: 336-341.
22. Davie JR, Spencer VA (1999) Control of histone modifications. J Cell Biochem Suppl 32-33: 141-148.
23. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279-284.
24. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
25. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
26. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
27. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
28. Lehner B, Fraser AG (2004) A first-draft human protein-interaction map. Genome Biol 5: R63.
29. Braha D, Bar-Yam Y (2004) Topology of large-scale engineering problem-solving networks. Phys Rev E 69: 1-7.
30. Ferrell JE Jr, Machleder EM (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280: 895-898.
31. Enver T, Heyworth CM, Dexter TM (1998) Do stem cells play dice? Blood 92: 348-351.
32. Graf T (2002) Differentiation plasticity of hematopoietic cells. Blood 99: 3089-3101.
33. Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, et al. (2002) Overview of the alliance for cellular signaling. Nature 420: 703-706.
34. Kohonen T (2001) Self-organizing maps. Heidelberg, Germany: Springer. 501 p.
35. Eichler GS, Huang S, Ingber DE (2003) Gene Expression Dynamics Inspector (GEDI): For integrative analysis of expression profiles. Bioinformatics 19: 2321-2322.
36. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.