Analyzing the regulation of metabolic pathways in human breast cancer

BMC Medical Genomics

Volumn 3, Issue , 2010, Pages

  Schramm, Gunnar ^a   Surmann, Eva Maria ^a   Wiesberg, Stefan ^a   Oswald, Marcus ^a   Reinelt, Gerhard ^a   Eils, Roland ^a,b   König, Rainer ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BILE ACID METABOLISM; BREAST CARCINOMA; CHOLESTEROL METABOLISM; CONTROLLED STUDY; DECOMPOSITION; FEMALE; FRUCTOSE METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE MAPPING; GENE NUMBER; GENE REGULATORY NETWORK; GENETIC SELECTION; GLYCOLYSIS; HUMAN; HUMAN CELL; LIPID DEGRADATION; METABOLIC REGULATION; MITOSIS; NUCLEOTIDE METABOLISM; PATTERN RECOGNITION; PRIORITY JOURNAL; PROTEIN MICROARRAY; PURINE METABOLISM; PYRIMIDINE METABOLISM; SIGNAL TRANSDUCTION; STEROIDOGENESIS; UPREGULATION; BIOSYNTHESIS; BREAST TUMOR; GENETICS; METABOLISM;

BILE ACID; ESTROGEN; STEROID;

BILE ACIDS AND SALTS; BREAST NEOPLASMS; ESTROGENS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; METABOLIC NETWORKS AND PATHWAYS; STEROIDS; UP-REGULATION;

EID: 77956461211     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-3-39     Document Type: Article

References (41)

1. New diagnostics and biological predictors of outcome in early breast cancer. C Oakman S Bessi E Zafarana F Galardi L Biganzoli A Di Leo, Breast Cancer Research 2009 205 1 11
2. Gene expression profiling predicts clinical outcome of breast cancer. LJ van 't Veer H Dai MJ van de Vijver YD He AA Hart M Mao HL Peterse K van der Kooy MJ Marton AT Witteveen GJ Schreiber RM Kerkhoven C Roberts PS Linsley R Bernards SH Friend, Nature 2002 415 530 536 10.1038/415530a 11823860
3. Polychemotherapy for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group. Lancet 1998 352 930 942 10.1016/S0140-6736(98)03301-7 9752815
4. Tamoxifen for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group. Lancet 1998 351 1451 1467 10.1016/S0140-6736(97)11423-4 9605801
5. A Gene-Expression Signature as a Predictor of Survival in Breast Cancer. MJ Van de Vijver YD He LJ van't Veer H Dai AAM Hart DW Voskuil GJ Schreiber JL Peterse C Roberts MJ Marton M Parrish D Atsma A Witteveen A Glas L Delahaye T van der Velde H Bartelink S Rodenhuis ET Rutgers SH Friend R Bernards, The New England Journal of Medicine 2002 347 1999 2009 10.1056/NEJMoa021967 12490681 (Pubitemid 35461656)
6. Concordance among Gene-Expression-Based Predictors for Breast Cancer. C Fan DS Oh L Wessels B Weigelt DSA Nuyten AB Nobel LJ van't Veer CM Perou, The New England Journal of Medicine 2006 355 560 569 10.1056/NEJMoa052933 16899776
7. Recent development of IMP dehydrogenase inhibitors for the treatment of cancer. L Chen KW Pankiewicz, Curr Opim Drug Discov Devel 2007 10 403 412
8. Biochemical pharmacology of acivicin in rat hepatoma cells. MS Lui, Biochem Pharamcol 1982 31 3469 3473 10.1016/0006-2952(82)90628-1 (Pubitemid 13234510)
9. Risk of acute nonlymphocytic leukemia and preleukemia in patients treated with cyclophosphamide for non-Hodgkin's lymphomas. Comparison with results obtained in patients treated for Hodgkin's disease and ovarian carcinoma with other alkylating agents. J Pedersen-Bjergaard, Ann Intern Med 1985 103 195 200 4014901
10. The Gene Ontology (GO) database and informatics resource. MA Harris J Clark A Ireland J Lomax M Ashburner R Foulger K Eilbeck S Lewis B Marshall C Mungall J Richter GM Rubin JA Blake C Bult M Dolan H Drabkin JT Eppig DP Hill L Ni M Ringwald R Balakrishnan JM Cherry KR Christie MC Costanzo SS Dwight S Engel DG Fisk JE Hirschman EL Hong RS Nash A Sethuraman CL Theesfeld D Botstein K Dolinski B Feierbach T Berardini S Mundodi SY Rhee R Apweiler D Barrell E Camon E Dimmer V Lee R Chisholm P Gaudet W Kibbe R Kishore EM Schwarz P Sternberg M Gwinn L Hannick J Wortman M Berriman V Wood N de la Cruz P Tonellato P Jaiswal T Seigfried R White, Nucleic Acids Res 2004 32 258 261 10.1093/nar/gkh066 14681407
11. KEGG for linking genomes to life and the environment. M Kanehisa M Araki S Goto M Hattori M Hirakawa M Itoh T Katayama S Kawashima S Okuda T Tokimatsu Y Yamanishi, Nucleic Acids Res 2008 36 480 484 10.1093/nar/gkm882 18077471
12. Significance tests which may be applied to samples from any population. EJG Pitman, Royal Statistical Society Supplement 1937 4 119 130 225-232 10.2307/2984124
13. A global test for groups of genes: testing association with a clinical outcome. JJ Goeman SA van de Geer F de Kort HC van Houwelingen, Bioinformatics 2004 20 93 99 10.1093/bioinformatics/btg382 14693814
14. Testing gene set enrichments for subset of genes: Sub-GSE. X Yan F Sun, BMC Bioinformatics 2008 9 1 15 10.1186/1471-2105-9-1 18173834
15. Uncovering transcriptional regulation of metabolism by using metabolic network topology. KR Patil J Nielsen, Proc Natl Acad Sci USA 2005 102 2685 2689 10.1073/pnas.0406811102 15710883
16. Network-based classification of breast cancer metastasis. HY Chuang E Lee YT Liu D Lee T Ideker, Mol Syst Biol 2007 3 140 10.1038/msb4100180 17940530
17. A network biology approach to prostate cancer. A Ergun CA Lawrence MA Kohanski TA Brennan JJ Collins, Mol Syst Biol 2007 3 82 10.1038/msb4100125 17299418
18. Classification of microarray data using gene networks. F Rapaport A Zinovyev M Dutreix E Barillot JP Vert, BMC Bioinformatics 2007 8 35 10.1186/1471-2105-8-35 17270037
19. Gene Expression Network Analysis, and Applications to Immunology. S Nacu R Critchley-Thorne P Lee S Holmes, Bioinformatics 2007 17267429
20. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. VK Mootha CM Lindgren KF Eriksson A Subramanian S Sihag J Lehar P Puigserver E Carlsson M Ridderstrale E Laurila N Houstis MJ Daly N Patterson JP Mesirov TR Golub P Tamayo B Spiegelman ES Lander JN Hirschhorn D Altshuler LC Groop, Nat Genet 2003 34 267 273 10.1038/ng1180 12808457
21. Regulation and function of ecto-5'-nucleotidase and adenosine in cancer. J Spychala, 39 th Meeting of the Polish Biochemical society 2003 185
22. Genes of glycolysis are ubiquitously overexpressed in 24 cancer classes. B Altenberg KO Greulich, Genomics 2004 84 1014 1020 10.1016/j.ygeno.2004.08.010 15533718
23. The role of the Crabtree effect and an endogenous fuel in the energy metabolism of resting and proliferating thymocytes. M Guppy E Greiner K Brand, Eur J Biochem 1993 212 95 99 10.1111/j.1432-1033.1993.tb17637.x 8444168
24. Cooperation and competition in the evolution of ATP-producing pathways. T Pfeiffer S Schuster S Bonhoeffer, Science 2001 292 504 507 10.1126/science. 1058079 11283355
25. Pyruvate into lactate and back: from the Warburg effect to symbiotic energy fuel exchange in cancer cells. O Feron, Radiother Oncol 2009 92 329 333 10.1016/j.radonc.2009.06.025 19604589
26. Understanding the Warburg effect: the metabolic requirements of cell proliferation. MG Vander Heiden LC Cantley CB Thompson, Science 2009 324 1029 1033 10.1126/science.1160809 19460998
27. Inhibition of glycolysis in cancer cells: a novel strategy to overcome drug resistance associated with mitochondrial respiratory defect and hypoxia. R Xu H Pelicano Y Zhou JS Carew L Feng KN Bhalla MJ Keating P Huang, Cancer Research 2005 65 613 621 10.1158/0008-5472.CAN-04-4313 15695406
28. Oxaloacetate induces DNA synthesis and Mitosis in primary cultured Rat Hepatocytes in the basence of EGF. Y Li, Biochemical and Biophysical Research communications 1993 193 1339 1346 10.1006/bbrc.1993.1772 8323554
29. Sex steroid-producing enzymes in human breast cancer. T Suzuki Y Miki Y Nakamura T Moriya K Ito N Ohuchi H Sasano, Endocrine-Related Cancer 2005 12 701 720 10.1677/erc.1.00834 16322318 (Pubitemid 41815772)
30. Bile acids and derivatives, their nuclear receptors FXR, PXR and ligands: role in health and disease and their therapeutic potential. A Zimber C Gespach, Anticancer Agents Med Chem 2008 8 540 563 18537536
31. The role of bile acids in carcinogenesis. PR Debruyne EA Bruyneel X Li A Zimber C Gespach MM Mareel, Mutat Res 2001 480-481 359 369 11506828
32. Deoxycholic acid activates beta-catenin signaling pathway and increases colon cell cancer growth and invasiveness. R Pai AS Tarnawski T Tran, Mol Biol Cell 2004 15 2156 2163 10.1091/mbc.E03-12-0894 15004225
33. Reduced bile acid-induced apoptosis in "normal" colorectal mucosa: a potential biological marker for cancer risk. H Garewal H Bernstein C Bernstein R Sampliner C Payne, Cancer Res 1996 56 1480 1483 8603388
34. Characterization of Enantiomeric Bile Acid-induced Apoptosis in Colon Cancer Cell Lines. BW Katona S Anant DF Covey WF Stenson, The journal of biological chemistry 2009 284 3354 3364 10.1074/jbc.M805804200 19054763
35. Inhibition of proliferation and induction of monocytic differentiation on HL60 human promyelocytic leukemia cells treated with bile acids in vitro. A Zimber A Chedeville C Gespach JP Abita, Int J Cancer 1994 59 71 77 10.1002/ijc.2910590115 7927907
36. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. S Loi B Haibe-Kains C Desmedt F Lallemand AM Tutt C Gillet P Ellis A Harris J Bergh JA Foekens JG Klijn D Larsimont M Buyse G Bontempi M Delorenzi MJ Piccart C Sotiriou, J Clin Oncol 2007 25 1239 1246 10.1200/JCO.2006.07.1522 17401012
37. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. S Loi B Haibe-Kains C Desmedt P Wirapati F Lallemand AM Tutt C Gillet P Ellis K Ryder JF Reid MG Daidone MA Pierotti EM Berns MP Jansen JA Foekens M Delorenzi G Bontempi MJ Piccart C Sotiriou, BMC Genomics 2008 9 239 10.1186/1471-2164-9-239 18498629
38. Outcome signature genes in breast cancer: is there a unique set? L Ein-Dor I Kela G Getz D Givol E Domany, Bioinformatics 2005 21 171 178 10.1093/bioinformatics/bth469 15308542
39. G Nemhauser L Wolsey, Integer and Combinatorial Optimization John Wiley & Sons, Hoboken 1999
40. Il calcolo delle assicurazioni su gruppi di test. CE Bonferroni, Studi in Onore del Professore Salvatore Ortu Carboni. Rome, Italy 1935 13 60
41. Simple solution to a common statistical problem: interpreting multiple tests. T Gordi H Khamis, Clin Ther 2004 26 780 786 10.1016/S0149-2918(04)90078-1 15220022