GATHER: A systems approach to interpreting genomic signatures

Bioinformatics

Volumn 22, Issue 23, 2006, Pages 2926-2933

  Chang, Jeffrey T ^a   Nevins, Joseph R ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RETINOBLASTOMA PROTEIN; TRANSCRIPTION FACTOR E2F;

ACCURACY; ARTICLE; BREAST CANCER; CANCER SURVIVAL; COMPUTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; INFORMATION PROCESSING; OUTCOMES RESEARCH; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

EID: 33751384465     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl483     Document Type: Article

References (47)

1. Al-Shahrour,F. et al. (2004) FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20, 578-580.
2. Allison,D.B. et al. (2006) Microarray data analysis: From disarray to consolidation, consensus. Nat. Rev. Genet., 7, 55-65.
3. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
4. Attwooll,C. et al. (2004) The E2F family: Specific functions and overlapping interests. EMBO J., 23, 4709-4716.
5. Bairoch,A. and Boeckmann,B. (1991) The SWISS-PROT protein sequence data bank. Nucleic Acids Res., 19, 2247-2249.
6. Barrett,T. et al. (2005) NCBI GEO: Mining millions of expression profiles - database and tools. Nucleic Acids Res., 33, D562-D566.
7. Bild,A.H. et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439, 353-357.
8. Black,E.P. et al. (2003) Distinct gene expression phenotypes of cells lacking Rb, Rb family members. Cancer Res., 63, 3716-3723.
9. Chaussepied,M. and Ginsberg,D. (2004) Transcriptional regulation of AKT activation by E2F. Mol. Cell., 16, 831-837.
10. 1/S regulatory genes. Mol. Cell. Biol., 15, 4215-4224.
11. Dimova,D.K. and Dyson,N.J. (2005) The E2F transcriptional network: Old acquaintances with new faces. Oncogene, 24, 2810-2826.
12. Ein-Dor,L. et al. (2005) Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics, 21, 171-178.
13. Gelman,A. et al. (2003) Bayesian Data Analysis. CRC Press LLC, Boca Raton, FL, USA.
14. Giangrande,P.H. et al. (2003) Identification of E-box factor TFE3 as a functional partner for the E2F3 transcription factor. Mol. Cell. Biol., 23, 3707-3720.
15. Golub,T.R. et al. (1999) Molecular classification of cancer: Class discovery, class prediction by gene expression monitoring. Science, 286, 531-537.
16. Hallstrom,T.C. and Nevins,J.R. (2003) Specificity in the activation and control of transcription factor E2F-dependent apoptosis. Proc. Natl Acad. Sci. USA., 100, 10848-10853.
17. Helin,K. (1998) Regulation of cell proliferation by the E2F transcription factors. Curr. Opin. Genet. Dev., 8, 28-35.
18. Hoffmann,R. and Valencia,A. (2004) A gene network for navigating the literature. Nat. Genet., 36, 664.
19. Ishida,S. et al. (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol., 21, 4684-4699.
20. Jenssen,T.K. et al. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
21. Karlseder,J. et al. (1996) Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F. Mol. Cell. Biol., 16, 1659-1667.
22. Kirschner,M.W. (2005) The meaning of systems biology. Cell, 121, 503-504.
23. Leone,G. et al. (1998) E2F3 activity is regulated during the cell cycle, is required for the induction of S phase. Genes Dev., 12, 2120-2130.
24. Linhart,C. et al. (2005) Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle, 4, 1788-1797.
25. Liu,K. et al. (2003) Regulation of E2F1 by BRCT domain-containing protein TopBP1. Mol. Cell. Biol., 23, 3287-3304.
26. Mootha,V.K. et al. (2003) PCC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
27. Moroni,M.C. et al. (2001) Apaf-1 is a transcriptional target for E2F, p53. Nat. Cell. Bio., 3, 552-558.
28. Muller,H. et al. (2001) E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev., 15, 267-285.
29. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences, structures. J. Mol. Biol., 247, 536-540.
30. Neufeld,T.P. et al. (1998) Coordination of growth and cell division in the Drosophila wing. Cell, 93, 1183-1193.
31. Nevins,J.R. (1998) Toward an understanding of the functional complexity of the E2F and retinoblastoma families. Cell Growth Differ., 9, 585-593.
32. Ohtani,K. et al. (1996) Expression of the HsOrc1 gene, a human ORC1 homolog, is regulated by cell proliferation via the E2F transcription factor. Mol. Cell. Biol., 16, 6977-6984.
33. Petricoin,E.F. et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet, 359, 572-577.
34. Polager,S. et al. (2002) E2Fs up-regulate expression of genes involved in DNA replication, DNA repair and mitosis. Oncogene, 21, 437-446.
35. 2/M checkpoints. Genes Dev., 16, 245-256.
36. Rhodes,D.R. et al. (2005) Mining for regulatory programs in the cancer transcriptome. Nat. Genet., 37, 579-583.
37. Rual,J.F. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
38. Schlisio,S. et al. (2002) Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function. EMBO J., 21, 5775-5786.
39. Sherr,C.J. (1996) Cancer cell cycles. Science, 274, 1672-1677.
40. Stelzl,U. et al. (2005) A human protein-protein interaction network: A resource for annotating the proteome. Cell, 122, 957-968.
41. Subramanian,A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
42. van't Veer,L.J. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
43. Wheeler,D.L. et al. (2001) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 29, 11-16.
44. Young,A.P. et al. (2003) Mechanisms of transcriptional regulation by Rb-E2F segregate by biological pathway. Oncogene, 22, 7209-7217.
45. Zeeberg,B.R. et al. (2003) GoMiner: A resource for biological interpretation of genomic and proteomic data. Genome Biol., 4, R28.
46. Zhang,B. et al. (2005) WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res., 33, W741-W748.
47. 2/M transcription. EMBO J., 23, 4615-4626.