An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer

Journal of the American Medical Informatics Association

Volumn 20, Issue 4, 2013, Pages 659-667

  Wen, Zhenshu ^a,b,c   Liu, Zhi Ping ^a   Liu, Zhengrong ^c   Zhang, Yan ^a   Chen, Luonan ^a,d  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b HUAQIAO UNIVERSITY   (China)

^c SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^d INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSIS; ARTICLE; CELL COMMUNICATION; CELL DIVISION; CELL PROLIFERATION; COLORECTAL CANCER; CONTROLLED STUDY; DISEASE COURSE; DISEASE MARKER; DNA METHYLATION; DNA REPAIR; GENE EXPRESSION; PATHOGENESIS; PROTEIN PROTEIN INTERACTION; TUMOR GENE;

ALGORITHMS; COLORECTAL NEOPLASMS; DNA METHYLATION; GENE EXPRESSION; GENE REGULATORY NETWORKS; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC; TRANSCRIPTION FACTORS;

EID: 84883000768     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1136/amiajnl-2012-001168     Document Type: Article

References (68)

1. Hunter DJ. Gene-environment interactions in human diseases. Nat Rev Genet 2005;6:287-98.
2. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009;461:218-23.
3. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-11.
4. Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286:531-7.
5. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5:101-13.
6. Chen L, Wang RS, Zhang XS. Biomolecular networks: methods and applications in systems biology. Hoboken, New Jersey: John Wiley & Sons Inc, 2009.
7. Chen L, Wang R, Li C Aihara K. Modeling biomolecular networks in cells: structures and dynamics. London: Springer-Verlag, 2010.
8. de Lichtenberg U, Jensen LJ, Brunak S, et al. Dynamic complex formation during the yeast cell cycle. Science 2005;307:724-7.
9. Segal E, Shapira M, Regev A, et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003;34:166-76.
10. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-50.
11. Van Leene J, Hollunder J, et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 2010;6:397.
12. He D, Liu ZP, Honda M, et al. Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma. J Mol Cell Biol 2012;4:140-52.
13. Liu X, Liu ZP, Zhao XM, et al. Identifying disease genes and module biomarkers by differential interactions. J Am Med Inform Assoc 2012;19:241-8.
14. Song W, Wang JG, Yang Y, et al. Rewiring drug-activated p53-regulatory network from suppressing to promoting tumorigenesis. J Mol Cell Biol 2012;4:197-206.
15. Wen Z, Liu ZP, Yan Y, et al. Identifying responsive modules by mathematical programming an application to budding yeast cell cycle. PLoS One 2012;7:e41854.
16. Chen L, Liu R, Liu ZP, et al. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci Rep 2012;2:342.
17. Iorns E, Lord CJ, Turner N, et al. Utilizing RNA interference to enhance cancer drug discovery. Nat Rev Drug Discov 2007;6:556-68.
18. Akavia UD, Litvin O, Kim J, et al. An integrated approach to uncover drivers of cancer. Cell 2010;143:1005-17.
19. Schadt EE, Lamb J, Yang X, et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005;37:710-17.
20. Kim YA, Wuchty S, Przytycka TM. Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput Biol 2011;7:e1001095.
21. Aerts S, Lambrechts D, Maity S, et al. Gene prioritization through genomic data fusion. Nat Biotechnol 2006;24:537-44.
22. Lee Y, Yang X, Huang Y, et al. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol 2010;6:e1000730.
23. Hinoue T, Weisenberger DJ, Lange CP, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012;22:271-82.
24. Galamb O, Spisak S, Sipos F, et al. Reversal of gene expression changes in the colorectal normal-adenoma pathway by NS398 selective COX2 inhibitor. Br J Cancer 2010;102:765-73.
25. Alhopuro P, Sammalkorpi H, Niittymaki I, et al. Candidate driver genes in microsatellite-unstable colorectal cancer. Int J Cancer 2012;130:1558-66.
26. Sabates-Bellver J, Van der Flier LG, de Palo M, et al. Transcriptome profile of human colorectal adenomas. Mol Cancer Res 2007;5:1263-75.
27. Hong Y, Downey T, Eu KW, et al. A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics. Clin Exp Metastasis 2010;27:83-90.
28. Peri S, Navarro JD, Kristiansen TZ, et al. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 2004;32(Database issue): D497-501.
29. Stark C, Breitkreutz BJ, Reguly T, et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006;34(Database issue):D535-9.
30. Hermjakob H, Montecchi-Palazzi L, Lewington C, et al. IntAct: an open source molecular interaction database. Nucleic Acids Res 2004;32(Database issue):D452-5.
31. Ceol A, Chatr Aryamontri A, Licata L, et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010;38(Database issue):D532-9.
32. Matthews L, Gopinath G, Gillespie M, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009;37(Database issue): D619-22.
33. Bibikova M, Le J, Barnes B, et al. Genome-wide DNA methylation profiling using Infinium((R)) assay. Epigenomics 2009;1:177-200.
34. Gebhard C, Benner C, Ehrich M, et al. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res 2010;70:1398-407.
35. Futreal PA, Coin L, Marshall M, et al. A census of human cancer genes. Nat Rev Cancer 2004;4:177-83.
36. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002;30:1575-84.
37. Zhao XM, Wang RS, Chen L, et al. Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 2008;36:e48.
38. Poole EM, Curtin K, Hsu L, et al. Genetic variability in EGFR, Src and HER2 and risk of colorectal adenoma and cancer. Int J Mol Epidemiol Genet 2011;2:300-15.
39. Saito S, Kato J, Hiraoka S, et al. DNA methylation of colon mucosa in ulcerative colitis patients: correlation with inflammatory status. Inflamm Bowel Dis 2011;17:1955-65.
40. Mort R, Mo L, McEwan C, et al. Lack of involvement of nucleotide excision repair gene polymorphisms in colorectal cancer. Br J Cancer 2003;89:333-7.
41. Ikeda S, Sasazuki S, Natsukawa S, et al. Screening of 214 single nucleotide polymorphisms in 44 candidate cancer susceptibility genes: a case-control study on gastric and colorectal cancers in the Japanese population. Am J Gastroenterol 2008;103:1476-87.
42. Mockelmann N, von Schonfels W, Buch S, et al. Investigation of innate immunity genes CARD4, CARD8 and CARD15 as germline susceptibility factors for colorectal cancer. BMC Gastroenterol 2009;9:79.
43. Erreni M, Mantovani A, Allavena P. Tumor-associated macrophages (TAM) and inflammation in colorectal cancer. Cancer Microenviron 2011;4:141-54.
44. Huang WY, Berndt SI, Kang D, et al. Nucleotide excision repair gene polymorphisms and risk of advanced colorectal adenoma: XPC polymorphisms modify smoking-related risk. Cancer Epidemiol Biomarkers Prev 2006;15:306-11.
45. Kweekel DM, Antonini NF, Nortier JW, et al. Explorative study to identify novel candidate genes related to oxaliplatin efficacy and toxicity using a DNA repair array. Br J Cancer 2009;101:357-62.
46. Li N, Bu X, Wu P, et al. The "HER2-PI3K/Akt-FASN Axis" regulated malignant phenotype of colorectal cancer cells. Lipids 2012;47:403-11.
47. Honma N, Arai T, Takubo K, et al. Oestrogen receptor-beta CA repeat polymorphism is associated with incidence of colorectal cancer among females. Histopathology 2011;59:216-24.
48. de Angelis PM, Fjell B, Kravik KL, et al. Molecular characterizations of derivatives of HCT116 colorectal cancer cells that are resistant to the chemotherapeutic agent 5-fluorouracil. Int J Oncol 2004;24:1279-88.
49. Guda K, Moinova H, He J, et al. Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers. Proc Natl Acad Sci U S A 2009;106:12921-5.
50. Curtin K, Wolff RK, Herrick JS, et al. Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor. BMC Med Genet 2010;11:170.
51. Pechlivanis S, Bermejo JL, Pardini B, et al. Genetic variation in adipokine genes and risk of colorectal cancer. Eur J Endocrinol 2009;160:933-40.
52. de Vogel S, Wouters KA, Gottschalk RW, et al. Genetic variants of methyl metabolizing enzymes and epigenetic regulators: associations with promoter CpG island hypermethylation in colorectal cancer. Cancer Epidemiol Biomarkers Prev 2009;18:3086-96.
53. Slattery ML, Herrick JS, Lundgreen A, et al. Genetic variation in a metabolic signaling pathway and colon and rectal cancer risk: mTOR, PTEN, STK11, RPKAA1, PRKAG2, TSC1, TSC2, PI3K and Akt1. Carcinogenesis 2010;31:1604-11.
54. Kraus S, Arber N. Inflammation and colorectal cancer. Curr Opin Pharmacol 2009;9:405-10.
55. Wood LD, Parsons DW, Jones S, et al. The genomic landscapes of human breast and colorectal cancers. Science 2007;318:1108-13.
56. Reimand J, Kull M, Peterson H, et al. g:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 2007;35(Web Server issue):W193-200.
57. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144:646-74.
58. Cavallo F, De Giovanni C, Nanni P, et al. 2011: the immune hallmarks of cancer. Cancer Immunol Immunother 2011;60:319-26.
59. Grossmann AH, Samowitz WS. Epidermal growth factor receptor pathway mutations and colorectal cancer therapy. Arch Pathol Lab Med 2011;135:1278-82.
60. Rizzo A, Pallone F, Monteleone G, et al. Intestinal inflammation and colorectal cancer: a double-edged sword? World J Gastroenterol 2011;17:3092-100.
61. Li J, Lenferink AE, Deng Y, et al. Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun 2010;1:34.
62. Jiang C, Xuan Z, Zhao F, et al. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 2007;35(Database issue): D137-40.
63. Gu S, Papadopoulou N, Nasir O, et al. Activation of membrane androgen receptors in colon cancer inhibits the prosurvival signals Akt/bad in vitro and in vivo and blocks migration via vinculin/actin signaling. Mol Med 2011;17:48-58.
64. Xu XL, Yu J, Zhang HY, et al. Methylation profile of the promoter CpG islands of 31 genes that may contribute to colorectal carcinogenesis. World J Gastroenterol 2004;10:3441-54.
65. Oster B, Thorsen K, Lamy P, et al. Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int J Cancer 2011;129:2855-66.
66. Kanai M, Hamada J, Takada M, et al. Aberrant expressions of HOX genes in colorectal and hepatocellular carcinomas. Oncol Rep 2010;23:843-51.
67. Cassinotti E, Melson J, Liggett T, et al. DNA methylation patterns in blood of patients with colorectal cancer and adenomatous colorectal polyps. Int J Cancer 2012;131:1153-7.
68. Hu B, Elinav E, Flavell RA. Inflammasome-mediated suppression of inflammation-induced colorectal cancer progression is mediated by direct regulation of epithelial cell proliferation. Cell Cycle 2011;10:1936-9.