54
Views
9
CrossRef citations to date
0
Altmetric
Original Articles

Detection of Activity Centers in Cellular Pathways Using Transcript Profiling

, , , , , , , , , , , , , , , & show all
Pages 701-721 | Received 01 Jan 2003, Accepted 01 Sep 2003, Published online: 02 Feb 2007

References

  • Albert , R. and Barabasi , A. L. 2002 . Statistical mechanics of complex networks . Rev. Modern Phys. , 74 ( 47 ) : 47 – 97 .
  • Alland , L. , Muhle , R. , Hou , H. Jr , Potes , J. , Chin , L. , Schreiber-Agus , N. and DePinho , R. A. 1997 . Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression . Nature , 387 ( 6628 ) : 49 – 55 . [CROSSREF]
  • Amin , N. S. , Nguyen , M. N. , Oh , S. and Kolodner , R. D. 2001 . Exo1-Dependent mutator mutations: Model system for studying functional interactions in mismatch repair . Mol. Cell. Biol. , 21 ( 15 ) : 5142 – 5155 . [CROSSREF]
  • Badie , C. , Itzhaki , J. E. , Sullivan , M. J. , Carpenter , A. J. and Porter , A. C. 2000 . Repression of CDK1 and other genes with CDE and CHR promoter elements during DNA damage-induced G2/M arrest in human cells . Mol. Cell. Biol. , 20 ( 7 ) : 2358 – 2366 . [CROSSREF]
  • Basalaj , W. 2001 . Proximity Visualization of Abstract Data, Technical Report 509, University of Cambridge Computer Laboratory, http://www.pavis.org/essay/ index.html
  • Blackwell , T. K. , Huang , J. , Ma , A. , Kretzner , L. , Alt , F. W. , Eisenman , R. N. and Weintraub , H. 1993 . Binding of myc proteins to canonical and noncanonical DNA sequences . Mol. Cell. Biol. , 13 ( 9 ) : 5216 – 5224 .
  • Blackwood , E. M. , Kretzner , L. and Eisenman , R. N. 1992 . Myc and Max function as a nucleoprotein complex . Curr. Opin. Genet. Dev. , 2 ( 2 ) : 227 – 235 .
  • Borg , I. and Groenen , P. 1997 . Modern Multidimensional Scaling: Theory and Applications , Springer Verlag Series in Statistics New York : Springer .
  • Brotherton , D. H. , Dhanaraj , V. , Wick , S. , Brizuela , L. , Domaille , P. J. , Volyanik , E. , Xu , X. , Parisini , E. , Smith , B. O. , Archer , S. J. , Serrano , M. , Brenner , S. L. , Blundell , T. L. and Laue , E. D. 1998 . Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d . Nature , 395 ( 6699 ) : 244 – 250 . [CROSSREF]
  • Buick , R. N. , Pullano , R. and Trent , J. M. 1985 . Comparative properties of five human ovarian adenocarcinoma cell lines . Cancer Res. , 45 ( 8 ) : 3668 – 3676 .
  • Chan , T. A. , Hermeking , H. , Lengauer , C. , Kinzler , K. W. and Vogelstein , B. 1999 . 14-3-3 sigma is required to prevent mitotic catastrophe after DNA damage . Nature , 401 ( 6753 ) : 616 – 620 . [CROSSREF]
  • Chen , Y. , Sharp , Z. D. and Lee , W. H. 1997 . HEC binds to the seventh regulatory subunit of the 26 S proteasome and modulates the proteolysis of mitotic cyclins . J. Biol. Chem. , 272 ( 28 ) : 24081 – 24087 . [CROSSREF]
  • Chiang , L. W. , Grenier , J. M. , Ettwiller , L. , Jenkins , L. P. , Ficenec , D. , Martin , J. , Jin , F. , DiStefano , P. S. and Wood , A. 2001 . An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis . Proc. Natl. Acad. Sci. U.S.A. , 98 ( 5 ) : 2814 – 2819 . [CROSSREF] [CSA]
  • Dang , C. V. 1999 . c-Myc target genes involved in cell growth, apoptosis, and metabolism . Mol. Cell. Biol. , 19 ( 1 ) : 1 – 11 .
  • DeRisi , J. L. , Iyer , V. R. and Brown , P. O. 1997 . Exploring the metabolic and genetic control of gene expression on a genomic scale . Science , 278 ( 5338 ) : 680 – 686 . [CROSSREF]
  • Eriksson , S. , Graslund , A. , Skog , S. , Thelander , L. and Tribukait , B. 1984 . Cell cycledependent regulation of mammalian ribonucleotide reductase. The S phase-correlated increase in subunit M2 is regulated by de novo protein synthesis . J. Biol. Chem. , 259 ( 19 ) : 11695 – 11700 .
  • Flatt , P. M. and Pietenpol , J. A. 2000 . Mechanisms of cell-cycle checkpoints: At the crossroads of carcinogenesis and drug discovery . Drug. Metab. Rev. , 32 ( 3-4 ) : 283 – 305 . [CROSSREF] [CSA]
  • Gaubatz , S. , Imhof , A. , Dosch , R. , Werner , O. , Mitchell , P. , Buettner , R. and Eilers , M. 1995 . Transcriptional activation by Myc is under negative control by the transcription factor AP-2 . EMBO J. , 14 ( 7 ) : 1508 – 1519 . [CSA]
  • Ge , H. , Liu , Z. , Church , G. M. and Vidal , M. 2001 . Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae . Nat. Genet. , 29 ( 4 ) : 482 – 486 . [CROSSREF]
  • Goto , S. , Nishioka , T. and Kanehisa , M. 1998 . LIGAND: Chemical database for enzyme reactions . Bioinformatics , 14 ( 7 ) : 591 – 599 . [CROSSREF] [CSA]
  • Grigoriev , A. 2001 . A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae . Nucleic Acids Res. , 29 ( 17 ) : 3513 – 3519 . [CROSSREF]
  • Gupta , S. , Seth , A. and Davis , R. J. 1993 . Transactivation of gene expression by Myc is inhibited by mutation at the phosphorylation sites Thr-58 and Ser-62 . Proc. Natl. Acad. Sci. U.S.A. , 90 ( 8 ) : 3216 – 3220 . [CSA]
  • He , T. C. , Sparks , A. B. , Rago , C. , Hermeking , H. , Zawel , L. , da Costa , L. T. , Morin , P. J. , Vogelstein , B. and Kinzler , K. W. 1998 . Identification of c-MYC as a target of the APC pathway . Science , 281 ( 5382 ) : 1509 – 1512 . [CROSSREF]
  • Hermeking , H. , Lengauer , C. , Polyak , K. , He , T. C. , Zhang , L. , Thiagalingam , S. , Kinzler , K. W. and Vogelstein , B. 1997 . 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression . Mol. Cell. , 1 ( 1 ) : 3 – 11 . [CROSSREF]
  • Imamura , T. , Izumi , H. , Nagatani , G. , Ise , T. , Nomoto , M. , Iwamoto , Y. and Kohno , K. 2001 . Interaction with p53 enhances binding of cisplatin-modified DNA by High Mobility Group 1 protein . J. Biol. Chem. , 276 ( 10 ) : 7534 – 7540 . [CROSSREF]
  • Jansen , R. , Greenbaum , D. and Gerstein , M. 2002 . Relating whole-genome expression data with protein-protein interactions . Genome Res. , 12 ( 1 ) : 37 – 46 . [CROSSREF] [CSA]
  • Kawabe , T. , Tsuyama , N. , Kitao , S. , Nishikawa , K. , Shimamoto , A. , Shiratori , M. , Matsumoto , T. , Anno , K. , Sato , T. , Mitsui , Y. , Seki , M. , Enomoto , T. , Goto , M. , Ellis , N. A. , Ide , T. , Furuichi , Y. and Sugimoto , M. 2000 . Differential regulation of human RecQ family helicases in cell transformation and cell cycle . Oncogene , 19 ( 41 ) : 4764 – 4772 . [CROSSREF] [CSA]
  • Kohn , K. W. 1999 . Molecular interaction map of the mammalian cell cycle control and DNA repair systems . Mol. Biol. Cell , 10 ( 8 ) : 2703 – 2734 . [CSA]
  • Leach , S. D. , Scatena , C. D. , Keefer , C. J. , Goodman , H. A. , Song , S. Y. , Yang , L. and Pietenpol , J. A. 1998 . Negative regulation of Wee1 expression and Cdc2 phosphorylation during p53-mediated growth arrest and apoptosis . Cancer Res. , 58 ( 15 ) : 3231 – 3236 .
  • Levine , A. J. 1997 . p53, the cellular gatekeeper for growth and division . Cell , 88 ( 3 ) : 323 – 333 . [CROSSREF]
  • Matton , N. , Simonetti , J. and Williams , K. 2000 . Identification of mismatch repair protein complexes in HeLa nuclear extracts and their interaction with heteroduplex DNA . J. Biol. Chem. , 275 ( 23 ) : 17808 – 17813 . [CROSSREF]
  • Miki , R. , Kadota , K. , Bono , H. , Mizuno , Y. , Tomaru , Y. , Carninci , P. , Itoh , M. , Shibata , K. , Kawai , J. , Konno , H. , Watanabe , S. , Sato , K. , Tokusumi , Y. , Kikuchi , N. , Ishii , Y. , Hamaguchi , Y. , Nishizuka , I. , Goto , H. , Nitanda , H. , Satomi , S. , Yoshiki , A. , Kusakabe , M. , DeRisi , J. L. , Eisen , M. B. , Iyer , V. R. , Brown , P. O. , Muramatsu , M. , Shimada , H. , Okazaki , Y. and Hayashizaki , Y. 2001 . Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays . Proc. Natl. Acad. Sci. U.S.A. , 98 ( 5 ) : 2199 – 2204 . [CROSSREF] [CSA]
  • Mills , J. C. , Stone , N. L. , Erhardt , J. and Pittman , R. N. 1998 . Apoptotic membrane blebbing is regulated by myosin light chain phosphorylation . J. Cell. Biol. , 140 ( 3 ) : 627 – 636 . [CROSSREF]
  • Newman , M. E. 2002 . Assortative mixing in networks . Phys. Rev. Lett. , 89 ( 20 ) : 208701 [CROSSREF]
  • Newman , M. E. , Strogatz , S. H. and Watts , D. J. 2001 . Random graphs with arbitrary degree distributions and their applications . Phys. Rev. E , 64 ( 2-2 ) : 026118 [CROSSREF]
  • Phang , J. M. 1985 . The regulatory functions of proline and pyrroline-5-carboxylic acid . Curr. Top. Cell. Regul. , 25 : 91 – 132 .
  • Ravasz , E. , Somera , A. L. , Mongru , D. A. , Oltvai , Z. N. and Barabasi , A. L. 2002 . Hierarchical organization of modularity in metabolic networks . Science , 297 ( 5586 ) : 1551 – 1555 . [CROSSREF]
  • Rocke , D. M. and Durbin , B. 2003 . Approximate variance-stabilizing transformations for gene-expression microarray data . Bioinformatics , 19 ( 8 ) : 966 – 972 . [CROSSREF] [CSA]
  • Simbulan , C. M. , Suzuki , M. , Izuta , S. , Sakurai , T. , Savoysky , E. , Kojima , K. , Miyahara , K. , Shizuta , Y. and Yoshida , S. 1993 . Poly(ADP-ribose) polymerase stimulates DNA polymerase alpha by physical association . J. Biol. Chem. , 268 ( 1 ) : 93 – 99 .
  • Takai-Igarashi , T. and Kaminuma , T. 1999 . A pathway finding system for the cell signaling networks database . In Silico Biol. , 1 ( 3 ) : 129 – 146 . [CSA]
  • Townsley , F. M. , Aristarkhov , A. , Beck , S. , Hershko , A. and Ruderman , J. V. 1997 . Dominant-negative cyclin-selective ubiquitin carrier protein E2-C/UbcH10 blocks cells in metaphase . Proc. Natl. Acad. Sci. U.S.A. , 94 ( 6 ) : 2362 – 2367 . [CROSSREF] [CSA]
  • Watts , D. J. and Strogatz , S. H. 1998 . Collective dynamics of “small-world” networks . Nature , 393 ( 6684 ) : 440 – 442 . [CROSSREF]
  • Weber , J. D. , Taylor , L. J. , Roussel , M. F. , Sherr , C. J. and Bar-Sagi , D. 1999 . Nucleolar Arf sequesters Mdm2 and activates p53 . Nat. Cell. Biol. , 1 ( 1 ) : 20 – 26 . [CROSSREF]
  • Wesierska-Gadek , J. and Schmid , G. 2000 . Overexpressed poly(ADP-ribose) polymerase delays the release of rat cells from p53-mediated G1 checkpoint . J. Cell. Biochem. , 80 ( 1 ) : 85 – 103 . [CROSSREF]
  • Zhao , R. , Gish , K. , Murphy , M. , Yin , Y. , Notterman , D. , Hoffman , W. H. , Tom , E. , Mack , D. H. and Levine , A. J. 2000 . Analysis of p53-regulated gene expression patterns using oligonucleotide arrays . Genes Dev. , 14 ( 8 ) : 981 – 993 . [CROSSREF]
  • Zhong , Q. , Chen , C. F. , Li , S. , Chen , Y. , Wang , C. C. , Xiao , J. , Chen , P. L. , Sharp , Z. D. and Lee , W. H. 1999 . Association of BRCA1 with the hRad50-hMre11-p95 complex and the DNA damage response . Science , 285 : 747 – 750 . [CROSSREF]

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.