Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3151-3157

  Nam, Hojung ^a   Chung, Bong Chul ^b   Kim, Younghoon ^a   Lee, KiYoung ^c   Lee, Doheon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Korea Institute of Science and Technology   (South Korea)

^c Ajou University School of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

4 HYDROXYPHENYLACETIC ACID; 4-HYDROXYPHENYLACETATE; 5 HYDROXYINDOLEACETIC ACID; HOMOVANILLIC ACID; PHENYLACETIC ACID DERIVATIVE; TUMOR MARKER; UREA;

ARTICLE; BREAST TUMOR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METABOLOMICS; METHODOLOGY; PATHOLOGY; PROTEOMICS; RECEIVER OPERATING CHARACTERISTIC; URINE;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HOMOVANILLIC ACID; HUMANS; HYDROXYINDOLEACETIC ACID; METABOLOMICS; PHENYLACETATES; PROTEOMICS; ROC CURVE; TUMOR MARKERS, BIOLOGICAL; UREA;

EID: 75949130452     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp558     Document Type: Article

References (32)

1. Al-Majid, S. and Waters, H. (2008) The biological mechanisms of cancer-related skeletal muscle wasting: the role of progressive resistance exercise. Biol. Res. Nurs., 10, 7-20.
2. Argiles, J.M. et al. (2007) Mechanisms to explain wasting of muscle and fat in cancer cachexia. Curr. Opin. Support. Palliative Care, 1, 293-298.
3. Beckmann, M. et al. (2008) High-throughput, nontargeted metabolite fingerprinting using nominal mass flow injection electrospray mass spectrometry. Nature Protocols, 3, 486-504.
4. Berishaj, M. et al. (2007) Stat3 is tyrosine-phosphorylated through the interleukin-6/glycoprotein 130/Janus kinase pathway in breast cancer. Breast Cancer Res., 9, R32.
5. Deng, C. et al. (2004) Development of headspace solid-phase microextraction with on-fiber derivatization for determination of hexanal and heptanal in human blood. J. Chromatogr., 813, 47-52.
6. Denkert, C. et al. (2008) Metabolite profiling of human colon carcinoma-deregulation of TCA cycle and amino acid turnover. Mol. Cancer, 7, 72.
7. Dinu, I. et al. (2007) Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics, 8, 242.
8. Gatenby, R.A. and Gillies, R.J. (2004) Why do cancers have high aerobic glycolysis? Nat. Rev. Cancer, 4, 891-899.
9. Hall, R.K. et al. (2007) Insulin represses phosphoenolpyruvate carboxykinase gene transcription by causing the rapid disruption of an active transcription complex: a potential epigenetic effect. Mol. Endocrinol., 21, 550-563.
10. Henneges, C. et al. (2009) Prediction of breast cancer by profiling of urinary RNA metabolites using Support Vector Machine-based feature selection. BMC Cancer, 9, 104.
11. Holmes, E. et al. (2008) Human metabolic phenotype diversity and its association with diet and blood pressure. Nature, 453, 396-400.
12. Houssami, N. et al. (2002) The comparative sensitivity of mammography and ultrasound in women with breast symptoms: an age-specific analysis. Breast, 11, 125-130.
13. Jensen, A. et al. (2006) Performance of clinical mammography: a nationwide study from Denmark. Int. J. Cancer, 119, 183-191.
14. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
15. Kanehisa, M. et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34, D354-D357.
16. Kanehisa, M. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
17. Kim, J.W. and Dang, C.V. (2006) Cancer's molecular sweet tooth and the Warburg effect. Cancer Res., 66, 8927-8930.
18. Li, M. et al. (2008) Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl Acad. Sci. USA, 105, 2117-2122.
19. Matys, V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
20. Matys, V. et al. (2006)TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
21. Moreno-Sanchez, R. et al. (2007) Energy metabolism in tumor cells. FEBS J., 274, 1393-1418.
22. Nakamura, R. et al. (2005) Gene expression profiling of dexamethasone-treated RBL-2H3 cells: induction of anti-inflammatory molecules. Immunol. Lett., 98, 272-279.
23. Nam, H. et al. (2009) Computational identification of altered metabolism using gene expression and metabolic pathways. Biotechnol. Bioeng., 103, 835-843.
24. Phillips, M. et al. (2003) Volatile markers of breast cancer in the breath. Breast J., 9, 184-191.
25. Phillips, M. et al. (2006) Prediction of breast cancer using volatile biomarkers in the breath. Breast Cancer Res. Treat, 99, 19-21.
26. Poulter, J.M. et al. (1985) Tryptophan metabolism in patients with breast cancer. Acta Vitaminol. Enzymol., 7, 93-97.
27. Sigoillot, F.D. et al. (2004) Breakdown of the regulatory control of pyrimidine biosynthesis in human breast cancer cells. Internat. J. Cancer, 109, 491-498.
28. Sreekumar, A. et al. (2009) Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature, 457, 910-914.
29. Stein, S.E. (1999) An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J. Am. Soc. Mass Spectrom., 10, 770-781.
30. Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
31. Wishart, D.S. et al. (2007) HMDB: the human metabolome database. Nucleic Acids Res., 35, D521-D526.
32. Yeh, C.S. et al. (2006) Fatty acid metabolism pathway play an important role in carcinogenesis of human colorectal cancers by Microarray-Bioinformatics analysis. Cancer Lett., 233, 297-308.