Prestige centrality-based functional outlier detection in gene expression analysis

Bioinformatics

Volumn 25, Issue 17, 2009, Pages 2222-2228

  Torkamani, Ali ^a   Schork, Nicholas J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD24 ANTIGEN; HERMES ANTIGEN;

ALGORITHM; ARTICLE; CELL SUBPOPULATION; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE REGULATORY NETWORK; METASTASIS; PRIORITY JOURNAL;

ALGORITHMS; ANTIGENS, CD24; ANTIGENS, CD44; DISEASE-FREE SURVIVAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; NEOPLASM METASTASIS; ROC CURVE;

EID: 69949147240     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp388     Document Type: Article

References (45)

1. Abraham,B.K. et al. (2005) Prevalence of CD44+/CD24-/low cells in breast cancer may not be associated with clinical outcome but may favor distant metastasis. Clin. Cancer Res., 11, 1154-1159.
2. Al-Hajj,M. et al. (2003) Prospective identification of tumorigenic breast cancer cells. Proc. Natl Acad. Sci. USA, 100, 3983-3988.
3. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
4. Bild,A.H. et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature, 439, 353-357.
5. Bourdeau,V. et al. (2007) Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucleic Acids Res., 36, 76-93.
6. Butte,A. et al. (2000) Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl Acad. Sci. USA, 97, 12182-12186.
7. Cai,L. et al. (2006) Stochastic protein expression in individual cells at the single molecule level. Nature, 440, 358-362.
8. Carter,S. et al. (2004) Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics, 20, 2242-2250.
9. Cover,T.M. and Thomas,J.A. (1991) Elements of Information Theory. John Wiley & Sons, New York.
10. Duss,S. et al. (2007) An oestrogen-dependent model of breast cancer created by transformation of normal human mammary epithelial cells. Breast Cancer Res., 9, R38.
11. Horvath,S. and Dong,J. (2008) Geometric interpretation of gene coexpression network analysis. PLoS Comput. Biol., 4, e1000117.
12. Horvath,S. et al. (2006) Analysis of Oncogenic Signaling Networks in Glioblastoma Identifies ASPM as a Novel Molecular Target. Proc. Natl Acad. Sci. USA, 103, 17402-17407.
13. Huang,Y. et al. (2007) Epithelial to mesenchymal transition in human breast epithelial cells transformed by 17beta-estradiol. Cancer Res., 67, 11147-11157.
14. Ideker,T. and Sharan,R. (2008) Protein networks in disease. Genome Res., 18, 644-652.
15. Ikeda,K. et al. (2006) Glia maturation factor-gamma is preferentially expressed in microvascular endothelial and inflammatory cells and modulates actin cytoskeleton reorganization. Circ. Res., 99, 424-433.
16. Ince,T.A. et al. (2007) Transformation of different human breast epithelial cell types leads to distinct tumor phenotypes. Cancer Cell 12, 160-170.
17. Johnstone,C.N. et al. (2008) Parvin-beta inhibits breast cancer tumorigenicity and promotes CDK9-mediated peroxisome proliferator-activated receptor gamma 1 phosphorylation. Mol. Cell Biol., 28, 687-704.
18. Kaern,M. et al. (2005) Stochasticity in gene expression: From theories to phenotypes. Nat. Rev. Genet., 6, 451-464.
19. Kaufmann,B.B. and van Oudenaarden,A. (2007) Stochastic gene expression: from single molecules to the proteome. Curr. Opin. Genet. Dev., 17, 107-112.
20. Lasko,T.A. et al. (2005). The use of receiver operating characteristic curves in biomedical informatics. J. Biomed. Inform. 38, 404-415.
21. Lauss,M. et al. (2008) Consensus genes of the literature to predict breast cancer recurrence. Breast Cancer Res. Treat., 110, 235-244.
22. Lee,D.S. et al. (2008) The implications of human metabolic network topology for disease comorbidity. Proc. Natl Acad. Sci. USA, 105, 9880-9885.
23. Oldham,M.C. et al. (2008) Functional organization of the transcriptome in human brain. Nat. Neurosci., 11, 1271-1282.
24. Lewis,M.T. (2008) Faith, heresy and the cancer stem cell hypothesis. Future Oncol., 4, 585-589.
25. Liu,L. et al. (2005) LSP1 is an endothelial gatekeeper of leukocyte transendothelial migration. J. Exp. Med., 201, 409-418.
26. Liu,R. et al. (2007) The prognostic role of a gene signature from tumorigenic breast-cancer cells. N. Engl. J. Med., 356, 217-226.
27. Loi,S. et al. (2007) Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J. Clin. Oncol., 25, 1239-1246.
28. Mah,S.A. et al. (2004) A perforin-like protein from amarine mollusk. Biochem. Biophys. Res. Commun., 316, 468-475.
29. Mani,K.M. et al. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol. Syst. Biol., 4, 169.
30. Margolin,A.A. et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7, S7.
31. Massagué,J. (2007) Sorting out breast-cancer gene signatures. N. Engl. J. Med., 356, 294-297.
32. Richardson,A.L. et al. (2006) X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell, 9, 121-132.
33. Schuetz,C.S. et al. (2006) Progression-specific genes identified by expression profiling of matched ductal carcinomas in situ and invasive breast tumors, combining laser capture microdissection and oligonucleotide microarray analysis. Cancer Res., 66, 5278-5286.
34. Thiery,J.P. (2003) Epithelial-mesenchymal transitions in development and pathologies. Curr. Opin. Cell Biol., 15, 740-746.
35. Till,K.J. et al. (2002) The chemokine receptor CCR7 and alpha4 integrin are important for migration of chronic lymphocytic leukemia cells into lymph nodes. Blood 99, 2977-2984.
36. Trapani,J.A. and Smyth,M.J. (2002) Functional significance of the perforin/granzyme cell death pathway. Nat. Rev. Immunol., 2, 735-747.
37. Turashvili,G. et al. (2007) Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis. BMC Cancer, 7, 55.
38. Visvader,J.E. and Lindeman,G.J. (2008) Cancer stem cells in solid tumours: Accumulating evidence and unresolved questions. Nat. Rev. Cancer, 8, 755-768.
39. Volfson,D. et al. (2006) Origins of extrinsic variability in eukaryotic gene expression. Nature, 439, 861-864.
40. Wang,Y. (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet, 365, 671-679.
41. Wang,C. et al. (1998) The overexpression of RHAMM, a hyaluronan-binding protein that regulates ras signaling, correlates with overexpression of mitogen-activated protein kinase and is a significant parameter in breast cancer progression. Clin. Cancer Res., 4 567-576.
42. Wasserman,S. and Faust,K. (1994) Social Network Analysis: Methods and Applications. Cambridge University Press, Cambridge.
43. Weiner,O.D. et al. (2007) An actin-based wave generator organizes cell motility. PLoS Biol., 9, e221.
44. Zhang,B. and Horvath,S. (2005) A general framework for weighted gene co-expression network analysis. Statist. Appl. Genet. Mol. Biol., 4, Article 17.
45. Zhang,B. et al. (2004) GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 5, 16.