Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Westergaard, David ^a   Li, Jun ^a   Jensen, Kasper ^b   Kouskoumvekaki, Irene ^b   Panagiotou, Gianni ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

3 HYDROXY 3 METHYLGLUTARYL COENZYME A; BETA SOLAMARIN; CINNAMOYL COENZYME A; CLIONASTEROL; DIOCINE; FGR1 PROTEIN; GALLIC ACID; GLYCYRRHIZIC ACID; GSK3B PROTEIN; HSD17B1 PROTEIN; MARK1 PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE 14; NICOTIFLORIN; OLEOYL COENZYME A; PHYTOSTEROL; PLANT MEDICINAL PRODUCT; PRKACG PROTEIN; PROTEIN KINASE FYN; QUERCETIN; RUTOSIDE; SMAD3 PROTEIN; TEK PROTEIN; TOMATINE; TOP1 PROTEIN; TRANSSYLVANOSIDE C; TUMOR PROTEIN; UNCLASSIFIED DRUG; VASCULOTROPIN RECEPTOR 2;

ARTICLE; CANCER RISK; CANCER THERAPY; CLINICAL EFFECTIVENESS; COLON CANCER; CONTROLLED STUDY; CORIANDER; EATING HABIT; FOOD COMPOSITION; GLYCYRRHIZA; HUMAN; LIGAND BINDING; MEDICINAL PLANT; METABOLIC REGULATION; MOLECULAR INTERACTION; NUTRITIONAL ASSESSMENT; NUTRITIONAL SUPPORT; NUTRITIONAL VALUE; OUTCOME ASSESSMENT; PHYTOCHEMISTRY; POMEGRANATE; POTATO; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; RISK ASSESSMENT; ROSEMARY; SOYBEAN; THERAPY EFFECT; TOMATO; COLONIC NEOPLASMS; DIET; METABOLISM;

COLONIC NEOPLASMS; DIET; HUMANS; PHYTOCHEMICALS;

EID: 84902085281     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-380     Document Type: Article

References (28)

1. Kussmann M, Fay LB. Nutrigenomics and personalized nutrition: science and concept. Pers Med 2008, 5:447-455.
2. Kaput I. Nutrigenomics research for personalized nutrition and medicine. Curr Opin Biotechnol 2008, 19:110-120. 10.1016/j.copbio.2008.02.005, 18387295.
3. Hutter CM, Chang-Claude J, Slattery ML, Pflugeisen BM, Lin Y, Duggan D, Nan H, Lemire M, Rangrej J, Figueiredo JC, Jiao S, Harrison TA, Liu Y, Chen LS, Stelling DL, Warnick GS, Hoffmeister M, Küry S, Fuchs CS, Giovannucci E, Hazra A, Kraft P, Hunter DJ, Gallinger S, Zanke BW, Brenner H, Frank B, Ma J, Ulrich CM, White E, et al. Characterization of gene-environment interactions for colorectal cancer susceptibility loci. Cancer Res 2012, 72:2036-2044. 10.1158/0008-5472.CAN-11-4067, 3374720, 22367214.
4. Shiels PG, McGlynn LM, MacIntyre A, Johnson PC, Batty GD, Burns H, Cavanagh J, Deans KA, Ford I, McConnachie A, McGinty A, McLean JS, Millar K, Sattar N, Tannahill C, Velupillai YN, Packard CJ. Accelerated telomere attrition is associated with relative household income, diet, and inflammation of the pSoBid cohort. PLoS One 2011, 6:e22521. 10.1371/journal.pone.0022521, 3144896, 21818333.
5. Nanri H, Nakamura K, Hara M, Higaki Y, Imaizumi T, Taguchi N, Sakamoto T, Horita M, Shinchi K, Tanaka K. Association between dietary pattern and serum C-reactive protein in Japanese men and women. J Epidemiol 2011, 21:122-131. 10.2188/jea.JE20100110, 3899504, 21325731.
6. Manson MM. Cancer prevention- the potential for diet to modulate molecular signaling. Trends Mol Med 2003, 9:11-18. 10.1016/S1471-4914(02)00002-3, 12524205.
7. Katada S, Imhof A, Sassone-Corsi PL. Connecting threads: epigenetics and metabolism. Cell 2012, 148:24-28. 10.1016/j.cell.2012.01.001, 22265398.
8. Fu WJ, Stroberg AJ, Viele K, Carroll RJ, Wu G. Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology. J Nutr Biochem 2010, 21:561-572. 10.1016/j.jnutbio.2009.11.007, 2885517, 20233650.
9. Tammariello A, Milner J. Mouse models for unraveling the importance of diet in colon cancer prevention. J Nutr Biochem 2010, 21:77-88. 10.1016/j.jnutbio.2009.09.014, 2871384, 20122631.
10. Hambly R, Saunders M, Rijken PJ, Rowland IR. Influence of dietary components associated with high or low risk of colon cancer on apoptosis in the rat colon. Food Chem Toxicol 2002, 40:801-808. 10.1016/S0278-6915(02)00019-4, 11983275.
11. Jensen K, Panagiotou G, Kouskoumvekaki I. Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PLoS Comput Biol 2013, 10:e1003432.
12. Agren R, Bordel S, Mardinoglu A, Pomputtapong N, Nookaew I, Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 2012, 8:e1002518. 10.1371/journal.pcbi.1002518, 3355067, 22615553.
13. Oh SC, Park Y-Y, Park ES, Lim JY, Kim SM, Kim S-B, Kim J, Kim SC, Chu I-S, Smith JJ, Beauchamp RD, Yeatman TJ, Kopetz S, Lee J-S. Prognostic gene expression signature associated with two molecularly distinct subtypes of colorectal cancer. Gut 2012, 61:1291-1298. 10.1136/gutjnl-2011-300812, 3419333, 21997556.
14. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Bjorling L, Ponten F. Towards a Knowledge-Based Human Protein Atlas. Nat Biotech 2010, 28:1248-1250.
15. da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucelic Acids Res 2009, 37:1-13.
16. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 2012, 40:D306-D312. 10.1093/nar/gkr948, 3245097, 22096229.
17. Hsu PP, Sabatini DM. Cancer cell metabolism: warburg and beyond. Cell 2008, 134:703-707. 10.1016/j.cell.2008.08.021, 18775299.
18. Hu J, Locasale JW, Bielas JH, O'Sullivan JO, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D. Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat Biotech 2013, 31:522-529.
19. Wild CP. Future research perspectives on environment and health: the requirement for a more expansive concept of translational cancer research. Environ Health 2011, 10:S1-S15.
20. Heinrich J. Influence of indoor factors in dwellings on the development of childhood asthma. Int J Hyg Environ Health 2011, 214:1-25. 10.1016/j.ijheh.2010.08.009, 20851050.
21. Brook RD, Rajagopalan S, Pope CA, Brook JR, Bhatnagar A, Diez-Roux AV, Holguin F, Hong Y, Luepker RV, Mittleman MA, Peters A, Siscovick D, Smith SC, Whitsel L, Kaufman JD, American Heart Association Council on Epidemiology and Prevention, Council on the Kidney in Cardiovascular Disease, and Council on Nutrition, Physical Activity and Metabolism Particulate matter air pollution and cardiovascular disease: an update to the scientific statement from the American Heart Association. Circulation 2010, 121:2331-2378. 10.1161/CIR.0b013e3181dbece1, 20458016, American Heart Association Council on Epidemiology and Prevention, Council on the Kidney in Cardiovascular Disease, and Council on Nutrition, Physical Activity and Metabolism.
22. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS. DrugBank 3.0: a Comprehensive Resource for 'Omics' Research on Drugs. Nucleic Acids Res 2011, 39:D1035-D1041. 10.1093/nar/gkq1126, 3013709, 21059682.
23. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for Integration and Interpretation of Large-Scale Molecular Data Sets. Nucleic Acids Res 2012, 40:D109-D114. 10.1093/nar/gkr988, 3245020, 22080510.
24. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING V9.1: Protein-Protein Interaction Networks, with Increased Coverage and Integration. Nucleic Acids Res 2013, 41:D808-D815. 10.1093/nar/gks1094, 3531103, 23203871.
25. Bento AP, Gaulton A, Hersey A, Bellis J, Chambers J, Davies M, Kruger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP. The ChEMBL bioactivity database: an update. Nucleic Acids Res 2013, 42:D1083-D1090. 3965067, 24214965.
26. Kramer C, Kalliokoski T, Gedeck P, Vulpetti A. The Experimental Uncertainty of Heterogeneous Public K(i) Data. J Med Chem 2012, 55:5165-5173. 10.1021/jm300131x, 22643060.
27. Ertl P, Rohde B, Selzer P. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties. J Med Chem 2000, 43:3714-3717. 10.1021/jm000942e, 11020286.
28. Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B. KNIME: The Konstanz Information Miner. Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007) 2007, Heidelberg-Berlin: Springer-Verlag.