Mining for regulatory programs in the cancer transcriptome (original) (raw)
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). ArticleCAS Google Scholar
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. USA101, 9309–9314 (2004). ArticleCAS Google Scholar
Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nat. Genet.36, 1090–1098 (2004). ArticleCAS Google Scholar
Elkon, R., Linhart, C., Sharan, R., Shamir, R. & Shiloh, Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res.13, 773–780 (2003). ArticleCAS Google Scholar
Rhodes, D.R. et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia6, 1–6 (2004). ArticleCAS Google Scholar
Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res.31, 374–378 (2003). ArticleCAS Google Scholar
Sladek, F.M., Zhong, W.M., Lai, E. & Darnell, J.E. Jr. Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev.4, 2353–2365 (1990). ArticleCAS Google Scholar
Xanthopoulos, K.G. et al. The different tissue transcription patterns of gene for HNF-1, C/EBP, HNF-3, and HNF-4, protein factors that govern liver-specific transcription. Proc. Natl. Acad. Sci. USA88, 3807–3811 (1991). ArticleCAS Google Scholar
Black, B.L. & Olson, E.N. Transcriptional control of muscle development by myocyte enhancer factor-2 (MEF2) proteins. Annu. Rev. Cell Dev. Biol.14, 167–196 (1998). ArticleCAS Google Scholar
O'Donovan, K.J., Tourtellotte, W.G., Millbrandt, J. & Baraban, J.M. The EGR family of transcription-regulatory factors: progress at the interface of molecular and systems neuroscience. Trends Neurosci.22, 167–173 (1999). ArticleCAS Google Scholar
Taniguchi, T., Ogasawara, K., Takaoka, A. & Tanaka, N. IRF family of transcription factors as regulators of host defense. Annu. Rev. Immunol.19, 623–655 (2001). ArticleCAS Google Scholar
Caamano, J. & Hunter, C.A. NF-kappaB family of transcription factors: central regulators of innate and adaptive immune functions. Clin. Microbiol. Rev.15, 414–429 (2002). ArticleCAS Google Scholar
Rosner, M.H. et al. A POU-domain transcription factor in early stem cells and germ cells of the mammalian embryo. Nature345, 686–692 (1990). ArticleCAS Google Scholar
Nichols, J. et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell95, 379–391 (1998). ArticleCAS Google Scholar
La Thangue, N.B. The yin and yang of E2F-1: balancing life and death. Nat. Cell Biol.5, 587–589 (2003). ArticleCAS Google Scholar
Zhu, W., Giangrande, P.H. & Nevins, J.R. E2Fs link the control of G1/S and G2/M transcription. EMBO J.23, 4615–4626 (2004). ArticleCAS Google Scholar
Bracken, A.P. et al. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J.22, 5323–5335 (2003). ArticleCAS Google Scholar
Chae, H.D., Yun, J., Bang, Y.J. & Shin, D.Y. Cdk2-dependent phosphorylation of the NF-Y transcription factor is essential for the expression of the cell cycle-regulatory genes and cell cycle G1/S and G2/M transitions. Oncogene23, 4084–4088 (2004). ArticleCAS Google Scholar
Muller, H. et al. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev.15, 267–285 (2001). ArticleCAS Google Scholar
DeGregori, J., Kowalik, T. & Nevins, J.R. Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes. Mol. Cell Biol.15, 4215–4524 (1995). ArticleCAS Google Scholar
Keenan, S.M., Lents, N.H. & Baldassare, J.J. Expression of cyclin E renders cyclin D-CDK4 dispensable for inactivation of the retinoblastoma tumor suppressor protein, activation of E2F, and G1-S phase progression. J. Biol. Chem.279, 5387–5396 (2004). ArticleCAS Google Scholar
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science298, 1039–1043 (2002). ArticleCAS Google Scholar
Kleer, C.G. et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl. Acad. Sci. USA100, 11606–11611 (2003). ArticleCAS Google Scholar
Varambally, S. et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature419, 624–629 (2002). ArticleCAS Google Scholar
Gilmore, T.D., Kalaitzidis, D., Liang, M.C. & Starczynowski, D.T. The c-Rel transcription factor and B-cell proliferation: a deal with the devil. Oncogene23, 2275–2286 (2004). ArticleCAS Google Scholar
Houldsworth, J. et al. Relationship between REL amplification, REL function, and clinical and biologic features in diffuse large B-cell lymphomas. Blood103, 1862–1868 (2004). ArticleCAS Google Scholar
Lossos, I.S. et al. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Proc. Natl. Acad. Sci. USA99, 8886–8891 (2002). ArticleCAS Google Scholar
Nau, M.M. et al. L-myc, a new myc-related gene amplified and expressed in human small cell lung cancer. Nature318, 69–73 (1985). ArticleCAS Google Scholar
Wong, A.J. et al. Gene amplification of c-myc and N-myc in small cell carcinoma of the lung. Science233, 461–464 (1986). ArticleCAS Google Scholar
Zucman, J. et al. EWS and ATF-1 gene fusion induced by t(12;22) translocation in malignant melanoma of soft parts. Nat. Genet.4, 341–345 (1993). ArticleCAS Google Scholar
Jean, D. & Bar-Eli, M. Targeting the ATF-1/CREB transcription factors by single chain Fv fragment in human melanoma: potential modality for cancer therapy. Crit. Rev. Immunol.21, 275–286 (2001). ArticleCAS Google Scholar
Johnson, D.G., Cress, W.D., Jakoi, L. & Nevins, J.R. Oncogenic capacity of the E2F1 gene. Proc. Natl. Acad. Sci. USA91, 12823–12827 (1994). ArticleCAS Google Scholar
Schwab, M., Varmus, H.E. & Bishop, J.M. Human N-myc gene contributes to neoplastic transformation of mammalian cells in culture. Nature316, 160–162 (1985). ArticleCAS Google Scholar
Sylla, B.S. & Temin, H.M. Activation of oncogenicity of the c-rel proto-oncogene. Mol. Cell Biol.6, 4709–4716 (1986). ArticleCAS Google Scholar
Seth, A. & Papas, T.S. The c-ets-1 proto-oncogene has oncogenic activity and is positively autoregulated. Oncogene5, 1761–1767 (1990). CASPubMed Google Scholar
Lamb, J. et al. A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell114, 323–334 (2003). ArticleCAS Google Scholar