Biology Reference
In-Depth Information
31. Hastie T, Tibshirani R, Eisen MB et al . (2000) 'Gene shaving' as a method for
identifying distinct sets of genes with similar expression patterns. Genome Biol
1 : RESEARCH0003.
32. Tanay A, Sharan R, Shamir R. (2002) Discovering statistically significant biclus-
ters in gene expression data. Bioinformatics 18 (Suppl 1): S136-44.
33. Ihmels J, Bergmann S, Barkai N. (2004) Defining transcription modules using
large-scale gene expression data. Bioinformatics 20 : 1993-2003.
34. Bergmann S, Ihmels J, Barkai N. (2003) Iterative signature algorithm for the
analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter
Phys 67 : 031902.
35. Bergmann S, Ihmels J, Barkai N. (2004) Similarities and differences in genome-
wide expression data of six organisms. PLoS Biol 2 : E9.
36. Eisen MB, Spellman PT, Brown PO, Botstein D. (1998) Cluster analysis and dis-
play of genome-wide expression patterns. Proc Natl Acad Sci USA 95 : 14863-8.
37. Segal E, Shapira M, Regev A et al . (2003) Module networks: identifying regu-
latory modules and their condition-specific regulators from gene expression
data. Nat Genet 34 : 166-76.
38. Bar-Joseph Z, Gerber GK, Lee TI et al . (2003) Computational discovery of gene
modules and regulatory networks. Nat Biotechnol 21 : 1337-42.
39. Mootha VK, Lindgren CM, Eriksson KF et al . (2003) PGC-1alpha-responsive
genes involved in oxidative phosphorylation are coordinately downregulated in
human diabetes. Nat Genet 34 : 267-73.
40. Damian D, Gorfine M. (2004) Statistical concerns about the GSEA procedure.
Nat Genet 36 : 663; author reply 663.
41. Segal E, Friedman N, Koller D, Regev A. (2004) A module map showing
conditional activity of expression modules in cancer. Nat Genet 36 : 1090-8.
42. Lamb J, Ramaswamy S, Ford HL et al . (2003) A mechanism of cyclin D1 action
encoded in the patterns of gene expression in human cancer. Cell 114 : 323-34.
43. Rhodes DR, Yu J, Shanker K et al . (2004) Large-scale meta-analysis of cancer
microarray data identifies common transcriptional profiles of neoplastic transfor-
mation and progression. Proc Natl Acad Sci USA 101 : 9309-14.
44. Desai KV, Xiao N, Wang W et al . (2002) Initiating oncogenic event determines
gene-expression patterns of human breast cancer models. Proc Natl Acad Sci
USA 99 : 6967-72.
45. Chang CF, Wai KM, Patterton HG. (2004) Calculating the statistical signifi-
cance of physical clusters of co-regulated genes in the genome: the role of
chromatin in domain-wide gene regulation. Nucleic Acids Res 32 : 1798-807.
46. Gavin AC, Bösche M, Krause R et al . (2002) Functional organization of the
yeast proteome by systematic analysis of protein complexes. Nature 415 : 141-7.
47. Lee TI, Rinaldi NJ, Robert F et al . (2002) Transcriptional regulatory networks
in Saccharomyces cerevisiae . Science 298 : 799-804.
Search WWH ::




Custom Search