A module map showing conditional activity of expression modules in cancer (original) (raw)

References

  1. Ramaswamy, S., Ross, K.N., Lander, E.S. & Golub, T.R. A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49–54 (2003).
    Article CAS Google Scholar
  2. Ramaswamy, S. et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl. Acad. Sci. USA 98, 15149–15154 (2001).
    Article CAS Google Scholar
  3. Lamb, J. et al. A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell 114, 323–334 (2003).
    Article CAS Google Scholar
  4. Rhodes, D.R. et al. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc. Natl. Acad. Sci. USA 101, 9309–9314 (2004).
    Article CAS Google Scholar
  5. Mootha, V.K. et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267–723 (2003).
    Article CAS Google Scholar
  6. Su, A.I. et al. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA 99, 4465–4470 (2002).
    Article CAS Google Scholar
  7. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42–46 (2002).
    Article CAS Google Scholar
  8. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).
    Article CAS Google Scholar
  9. Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C. & Conklin, B.R. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31, 19–20 (2002).
    Article CAS Google Scholar
  10. Kim, S.C. et al. Constitutive activation of extracellular signal-regulated kinase in human acute leukemias: combined role of activation of MEK, hyperexpression of extracellular signal-regulated kinase, and downregulation of a phosphatase, PAC1. Blood 93, 3893–3899 (1999).
    CAS PubMed Google Scholar
  11. Chu, Y., Solski, P.A., Khosravi-Far, R., Der, C.J. & Kelly, K. The mitogen-activated protein kinase phosphatases PAC1, MKP-1, and MKP-2 have unique substrate specificities and reduced activity in vivo toward the ERK2 sevenmaker mutation. J. Biol. Chem. 271, 6497–6501 (1996).
    Article CAS Google Scholar
  12. Furukawa, T., Sunamura, M., Motoi, F., Matsuno, S. & Horii, A. Potential tumor suppressive pathway involving DUSP6/MKP-3 in pancreatic cancer. Am. J. Pathol. 162, 1807–1815 (2003).
    Article CAS Google Scholar
  13. Leone, A.M., Errico, M., Lin, S.L. & Cowen, D.S. Activation of extracellular signal-regulated kinase (ERK) and Akt by human serotonin 5-HT(1B) receptors in transfected BE(2)-C neuroblastoma cells is inhibited by RGS4. J. Neurochem. 75, 934–938 (2000).
    Article CAS Google Scholar
  14. Shi, C.S. et al. Regulator of G-protein signaling 3 (RGS3) inhibits Gbeta1gamma 2-induced inositol phosphate production, mitogen-activated protein kinase activation, and Akt activation. J. Biol. Chem. 276, 24293–24300 (2001).
    Article CAS Google Scholar
  15. Ge, B. et al. TAB1beta (transforming growth factor-beta-activated protein kinase 1-binding protein 1beta), a novel splicing variant of TAB1 that interacts with p38alpha but not TAK1. J. Biol. Chem. 278, 2286–2293 (2003).
    Article CAS Google Scholar
  16. Mita, H., Tsutsui, J., Takekawa, M., Witten, E.A. & Saito, H. Regulation of MTK1/MEKK4 kinase activity by its N-terminal autoinhibitory domain and GADD45 binding. Mol. Cell. Biol. 22, 4544–4555 (2002).
    Article CAS Google Scholar
  17. Granata, O.M. et al. Altered androgen metabolism eventually leads hepatocellular carcinoma to an impaired hormone responsiveness. Mol. Cell. Endocrinol. 193, 51–58 (2002).
    Article CAS Google Scholar
  18. Mundy, G.R. Metastasis to bone: causes, consequences and therapeutic opportunities. Nat. Rev. Cancer 2, 584–593 (2002).
    Article CAS Google Scholar
  19. Kang, Y. et al. A multigenic program mediating breast cancer metastasis to bone. Cancer Cell 3, 537–459 (2003).
    Article CAS Google Scholar
  20. Iguchi, H. et al. A possible role of VEGF in osteolytic bone metastasis of hepatocellular carcinoma. J. Exp. Clin. Cancer Res. 21, 309–313 (2002).
    CAS PubMed Google Scholar
  21. Boot, A.M., van den Heuvel-Eibrink, M.M., Hahlen, K., Krenning, E.P. & de Muinck Keizer-Schrama, S.M. Bone mineral density in children with acute lymphoblastic leukaemia. Eur. J. Cancer 35, 1693–1697 (1999).
    Article CAS Google Scholar
  22. Ugolini, F. et al. Differential expression assay of chromosome arm 8p genes identifies Frizzled-related (FRP1/FRZB) and Fibroblast Growth Factor Receptor 1 (FGFR1) as candidate breast cancer genes. Oncogene 18, 1903–1910 (1999).
    Article CAS Google Scholar
  23. Reinholz, M.M., Iturria, S.J., Ingle, J.N. & Roche, P.C. Differential gene expression of TGF-beta family members and osteopontin in breast tumor tissue: analysis by real-time quantitative PCR. Breast Cancer Res. Treat. 74, 255–269 (2002).
    Article CAS Google Scholar
  24. Bernards, R. & Weinberg, R.A. A progression puzzle. Nature 418, 823 (2002).
    Article CAS Google Scholar
  25. Hynes, R.O. Metastatic potential: generic predisposition of the primary tumor or rare, metastatic variants-or both? Cell 113, 821–823 (2003).
    Article CAS Google Scholar
  26. Ferrari, N. et al. DLX genes as targets of ALL-1: DLX 2,3,4 down-regulation in t(4;11) acute lymphoblastic leukemias. J. Leukoc. Biol. 74, 302–305 (2003).
    Article CAS Google Scholar
  27. Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166–176 (2003).
    Article CAS Google Scholar
  28. Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31, 370–377 (2002).
    Article CAS Google Scholar
  29. Tanay, A., Sharan, R., Kupiec, M. & Shamir, R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc. Natl. Acad. Sci. USA 101, 2981–2986 (2004).
    Article CAS Google Scholar
  30. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).
    Article CAS Google Scholar

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