Identifying grade/stage-related active modules in human co-regulatory networks: A case study for breast cancer

OMICS A Journal of Integrative Biology

Volumn 16, Issue 12, 2012, Pages 681-689

  Feng, Chenchen ^a   Chen, Lina ^a   Li, Wan ^a   Wang, Hong ^a   Zhang, Liangcai ^a   Jia, Xu ^a   Miao, Zhengqiang ^a   Qu, Xiaoli ^a   Li, Weiguo ^a   He, Weiming ^b  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ARTICLE; BREAST CANCER; CANCER GRADING; CANCER STAGING; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DISEASE SEVERITY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE REGULATORY NETWORK; HUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; SIMULATION; TUMOR GENE;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; NEOPLASM STAGING;

EID: 84870871455     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2012.0015     Document Type: Article

References (47)

1. Allred DC, Mohsin SK, and Fuqua SA. (2001). Histological and biological evolution of human premalignant breast disease. Endocr Relat Cancer 8, 47-61.
2. Baskin Y, and Yigitbasi T. (2010). Clinical proteomics of breast cancer. Curr Genomics 11, 528-536.
3. Bombonati A, and Sgroi DC. (2010). The molecular pathology of breast cancer progression. J Pathol 223, 307-317.
4. Chen L, Wang H, Zhang L, et al. (2010). Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. BMC Bioinformatics 11, 392.
5. Choi JA, Lee JW, Kim H, et al. (2010). Pro-survival of estrogen receptor-negative breast cancer cells is regulated by a BLT2- reactive oxygen species-linked signaling pathway. Carcinogenesis 31, 543-551.
6. Chuang HY, Lee E, Liu YT, Lee D, and Ideker T. (2007). Network- based classification of breast cancer metastasis. Mol Syst Biol 3, 140.
7. Colak R, Moser F, Chu JS, Schonhuth A, Chen N, and Ester M. (2010). Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks. PLoS One 5, e13348.
8. Dennis G Jr, Sherman BT, Hosack DA, et al. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4, P3.
9. Hamrita B, Ben Nasr H, Gabbouj S, Bouaouina N, Chouchane L, and Chahed K. (2010). Apolipoprotein A1 - 75 G/A and + 83 C/T polymorphisms: susceptibility and prognostic implications in breast cancer. Mol Biol Rep 38, 1637-1643.
10. Han CZ, Du LL, Jing JX, et al. (2008). Associations among lipids, leptin, and leptin receptor gene Gin223Arg polymorphisms and breast cancer in China. Biol Trace Elem Res 126, 38-48.
11. Hempel N, Ye H, Abessi B, Mian B, and Melendez JA. (2009). Altered redox status accompanies progression to metastatic human bladder cancer. Free Radic Biol Med 46, 42-50.
12. Hernandez-Vargas H, Ouzounova M, Le Calvez-Kelm F, et al. (2011). Methylome analysis reveals Jak-STAT pathway deregulation in putative breast cancer stem cells. Epigenetics 6, 428-439.
13. Huang da W, Sherman BT, and Lempicki RA. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57.
14. Ignatiadis M, and Sotiriou C. (2008). Understanding the molecular basis of histologic grade. Pathobiology 75, 104-111.
15. Jemal A, Siegel R, Ward E, et al. (2008). Cancer statistics, 2008. CA Cancer J Clin 58, 71-96.
16. Jeruss JS, Mittendorf EA, Tucker SL, et al. (2008). Staging of breast cancer in the neoadjuvant setting. Cancer Res 68, 6477- 6481.
17. Kempkensteffen C, Hinz S, Christoph F, et al. (2007). Expression parameters of the inhibitors of apoptosis cIAP1 and cIAP2 in renal cell carcinomas and their prognostic relevance. Int J Cancer 120, 1081-1086.
18. Kidokoro T, Tanikawa C, Furukawa Y, Katagiri T, Nakamura Y, and Matsuda K. (2008). CDC20, a potential cancer therapeutic target, is negatively regulated by p53. Oncogene 27, 1562-1571.
19. Klaholz BP, Mitschler A, and Moras D. (2000). Structural basis for isotype selectivity of the human retinoic acid nuclear receptor. J Mol Biol 302, 155-170.
20. Koyama H, Hibi T, Isogai Z, et al. (2007). Hyperproduction of hyaluronan in neu-induced mammary tumor accelerates angiogenesis through stromal cell recruitment: possible involvement of versican/PG-M. Am J Pathol 170, 1086-1099.
21. Lapointe J, Li C, Higgins JP, et al. (2004). Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA 101, 811-816.
22. Lerebours F, Vacher S, Andrieu C, Espie M, Marty M, Lidereau R, and Bieche I. (2008). NF-kappa B genes have a major role in inflammatory breast cancer. BMC Cancer 8, 41.
23. Li J, Lenferink AE, Deng Y, et al. (2010). Identification of highquality cancer prognostic markers and metastasis network modules. Nat Commun 1, 34.
24. Liu Y, Mayo MW, Nagji AS, et al. (2012). Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene 31, 1143-1154.
25. Ma XJ, Salunga R, Tuggle JT, et al. (2003). Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 100, 5974-5979.
26. Matys V, Fricke E, Geffers R, et al. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31, 374-378.
27. Mester J, and Redeuilh G. (2008). Proliferation of breast cancer cells: regulation, mediators, targets for therapy. Anticancer Agents Med Chem 8, 872-885.
28. Michalak P. (2008).Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91, 243-248.
29. Molloy AP, Martin FT, Dwyer RM, et al. (2009). Mesenchymal stem cell secretion of chemokines during differentiation into osteoblasts, and their potential role in mediating interactions with breast cancer cells. Int J Cancer 124, 326-332.
30. Peng X, Yun D, and Christov K. (2004). Breast cancer progression in MCF10A series of cell lines is associated with alterations in retinoic acid and retinoid X receptors and with differential response to retinoids. Int J Oncol 25, 961-971.
31. Peri S, Navarro JD, Kristiansen TZ, et al. (2004). Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32, D497-D501.
32. Perou CM, Sorlie T, Eisen MB, et al. (2000). Molecular portraits of human breast tumours. Nature 406, 747-752.
33. Purmann A, Toedling J, Schueler M, et al. (2007). Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics 89, 580-587.
34. Rakha EA, El-Sayed ME, Lee AH, et al. (2008). Prognostic significance of Nottingham histologic grade in invasive breast carcinoma. J Clin Oncol 26, 3153-3158.
35. Rakha EA, Reis-Filho JS, Baehner F, et al. (2010). Breast cancer prognostic classification in the molecular era: the role of histological grade. Breast Cancer Res 12, 207.
36. Ransohoff DF. (2004). Rules of evidence for cancer molecularmarker discovery and validation. Nat Rev Cancer 4, 309-314.
37. Schlotter CM, Vogt U, Allgayer H, and Brandt B. (2008). Molecular targeted therapies for breast cancer treatment. Breast Cancer Res 10, 211.
38. Segal E, Friedman N, Kaminski N, Regev A, and Koller D. (2005). From signatures to models: understanding cancer using microarrays. Nat Genet 37 Suppl, S38-S45.
39. Simon R, Radmacher MD, Dobbin K, and McShane LM. (2003). Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 95, 14-18.
40. Udabage L, Brownlee GR, Waltham M, et al. (2005). Antisensemediated suppression of hyaluronan synthase 2 inhibits the tumorigenesis and progression of breast cancer. Cancer Res 65, 6139-6150.
41. Vaclavicek A, Bermejo JL, Schmutzler RK, et al. (2007). Polymorphisms in the Janus kinase 2 (JAK)/signal transducer and activator of transcription (STAT) genes: putative association of the STAT gene region with familial breast cancer. Endocr Relat Cancer 14, 267-277.
42. Vant Veer LJ, Dai H, van de Vijver MJ, et al. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536.
43. Vegran F, Boidot R, Bonnetain F, Cadouot M, Chevrier S, and Lizard-Nacol S. (2011). Apoptosis gene signature of Survivin and its splice variant expression in breast carcinoma. Endocr Relat Cancer 18, 783-792.
44. Wang L, Zhang B, Wolfinger RD, and Chen X. (2008). An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet 4, e1000115.
45. Wang Y, Klijn JG, Zhang Y, et al. (2005). Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365, 671-679.
46. Wennmalm K, and Bergh J. (2011). A simple method for assigning genomic grade to individual breast tumours. BMC Cancer 11, 306.
47. Zhang J, Warren MA, Shoemaker SF, and Ip MM. (2007). NFkappaB1/p50 is not required for tumor necrosis factorstimulated growth of primary mammary epithelial cells: implications for NFkappaB2/p52 and RelB. Endocrinology 148, 268-278.