The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 256-

  Lin, Xue ^a   Afsari, Bahman ^a   Marchionni, Luigi ^b   Cope, Leslie ^b   Parmigiani, Giovanni ^b,c   Naiman, Daniel ^a   Geman, Donald ^a  

^a Johns Hopkins University   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INTERPRETATION; CLINICAL APPLICATION; COMPUTATIONAL BIOLOGY; DIFFERENTIALLY EXPRESSED GENE; EXPRESSION ANALYSIS; HIGH-THROUGHPUT DATA; MACHINE LEARNING APPROACHES; PROTEIN-PROTEIN INTERACTIONS;

BIOINFORMATICS; DISEASES; FORECASTING; PROTEINS;

GENE EXPRESSION;

BRCA1 PROTEIN; ESTROGEN RECEPTOR; PPP1CB PROTEIN; RNF14 PROTEIN; TUMOR MARKER; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; BREAST CANCER; CLASSIFIER; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE MUTATION; GENOMICS; MUTATIONAL ANALYSIS; PREDICTION; PROTEIN PROTEIN INTERACTION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, BRCA1; HUMANS; TUMOR MARKERS, BIOLOGICAL;

EID: 70349731768     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-256     Document Type: Article

References (47)

1. Marchionni L, Wilson R.F, Wolff A.C, Marinopoulos S, Parmigiani G, Bass E.B, Goodman S.N. Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med 2008, 148(5):358-369.
2. Gordon G.J, Jensen R.V, Hsiao L.L, Gullans S.R, Blumenstock J.E, Ramaswamy S, Richards W.G, Sugarbaker D.J, Bueno R. Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. Cancer Res 2002, 62(17):4963-4967.
3. Geman D, d'Avignon C, Naiman D.Q, Winslow R.L. Classifying gene expression profiles from pairwise mRNA comparisons. Stat Appl Genet Mol Biol 2004, 3. 1989150, 16646797.
4. Xu L, Tan A.C, Naiman D.Q, Geman D, Winslow R.L. Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics 2005, 21(20):3905-3911. 10.1093/bioinformatics/bti647, 16131522.
5. Tan A.C, Naiman D.Q, X L, Winslow R.L, Geman D. Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics 2005, 21(20):3896-3904. 10.1093/bioinformatics/bti631, 1987374, 16105897.
6. Xu L, Geman D, Winslow R.L. Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics 2007, 8:275. 10.1186/1471-2105-8-275, 1950528, 17663766.
7. Price N, Trent J, El-Naggar A, Cogdell D, Taylor E, Hunt K, Pollock R, Hood L, Shmulevich I, Zhang W. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leimyosarcomas. Proc Natl Acad Sci USA 2007, 102(43):15545-15550.
8. Raponi M, Lancet J.E, Fan H, Dossey L, Lee G, Gojo I, Feldman E.J, Gotlib J, Morris L.E, Greenberg P.L, Stone R.M, Porre P.D, Wang Y, Karp J.E. A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acute myeloid leukemia. Blood 2008, (5):2589-2596. 10.1182/blood-2007-09-112730, 18160667.
9. Kauff N.D, Offit K. Modeling genetic risk of breast cancer. JAMA 2007, 297(23):2637-2639. 10.1001/jama.297.23.2637, 17579233.
10. Whittemore A.S, Gong G, John E.M, McGuire V, Li F.P, Ostrow K.L, Dicioccio R, Felberg A, West D.W. Prevalence of BRCA1 mutation carriers among U.S. non- Hispanic Whites. Cancer Epidemiol Biomarkers Prev 2004, 13(12):2078-2083.
11. Ford D, Easton D.F, Stratton M, Narod S, Goldgar D, Devilee P, Bishop D.T, Weber B, Lenoir G, Chang-Claude J, Sobol H, Teare M.D, Struewing J, Arason A, Scherneck S, Peto J, Rebbeck T.R, Tonin P, Neuhausen S, Barkardottir R, Eyfjord J, Lynch H, Ponder B.A, Gayther S.A, Zelada-Hedman M. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 1998, 62(3):676-689. 10.1086/301749, 1376944, 9497246.
12. Walsh T, Casadei S, Coats K.H, Swisher E, Stray S.M, Higgins J, Roach K.C, Mandell J, Lee M.K, Ciernikova S, Foretova L, Soucek P, King M.C. Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. JAMA 2006, 295(12):1379-1388. 10.1001/jama.295.12.1379, 16551709.
13. van 't Veer L.J, Dai H, Vijver M.J, He Y.D, Hart A.A.M, Mao M, Peterse H.L, Kooy K, Marton M.J, Witteveen A.T, Schreiber G.J, Kerkhoven R.M, Roberts C, Linsley P.S, Bernards R, Friend S.H. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415(6871):530-536. 10.1038/415530a, 11823860.
14. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi O.P, Wilfond B, Borg A, Trent J, Raffeld M, Yakhini Z, Ben-Dor A, Dougherty E, Kononen J, Bubendorf L, Fehrle W, Pittaluga S, Gruvberger S, Loman N, Johannsson O, Olsson H, Sauter G. Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001, 344(8):539-548. 10.1056/NEJM200102223440801, 11207349.
15. Witten I, Frank E. Data Mining: Practical machine learning tools and techniques with Java implementations 2000,
16. Foulkes W, Stefansson I, Chappuis P, Bégin L, JR G, Wong N, Trudel M, Akslen L. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 2003, 95(19):1482-1485.
17. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron J.S, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou C, Lønning P.E, Brown P.O, Borresen-Dale A, Botstein D. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003, 100(14):8418-8423. 10.1073/pnas.0932692100, 166244, 12829800.
18. Osborne C.K. Steroid hormone receptors in breast cancer management. Breast Cancer Res Treat 1998, 51(3):227-238. 10.1023/A:1006132427948, 10068081.
19. Gruvberger S, Ringnér M, Chen Y, Panavally S, Saal L.H, A B, Fernö M, Peterson C, Meltzer P.S. Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 2001, 61(16):5979-5984.
20. Miller L, S J, George J, Vega V, Vergara L, Ploner A, Pawitan Y, PHall, Klaar S, Liu E.T, Bergh J. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 2005, 102(38):13550-13555. 10.1073/pnas.0506230102, 1197273,1197273, 16141321.
21. Sotiriou C, Wirapati P, Loi S, Harris A, F S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, de Vijver M.J.V, Bergh J, Piccart M, Delorenzi M. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006, 98(4):262-272.
22. ExpO Public Geo Datasets. , https://expo.intgen.org/geo/home.do
23. Rakha E.A, El-Sheikh S.E, Kandil M.A, El-Sayed M.E, Green A.R, Ellis I.O. Expression of BRCA1 protein in breast cancer and its prognostic significance. Hum Pathol 2008, 39(6):857-865. 10.1016/j.humpath.2007.10.011, 18400253.
24. Rosen E.M, Fan S, Pestell R.G, Goldberg I.D. BRCA1 gene in breast cancer. J Cell Physiol 2003, 196:19-41. 10.1002/jcp.10257, 12767038.
25. Park J.J, Irvine R.A, Buchanan G, Koh S.S, Park J.M, Tilley W.D, Stallcup M.R, Press M.F, Coetzee G.A. Breast cancer susceptibility gene 1 (BRCAI) is a coactivator of the androgen receptor. Cancer Res 2000, 60(21):5946-5949.
26. Yeh S, Hu Y.C, Rahman M, Lin H.K, Hsu C.L, Ting H.J, Kang H.Y, Chang C. Increase of androgen-induced cell death and androgen receptor transactivation by BRCA1 in prostate cancer cells. Proc Natl Acad Sci USA 2000, 97(21):11256-11261. 10.1073/pnas.190353897, 17187, 11016951.
27. Kuvbachieva A, Bestel A.M, FTissir, Maloum I, Guimiot F, Ramoz N, Bourgeois F, Moalic J.M, Goffinet A.M, Simonneau M. Identification of a novel brain-specific and Reelin-regulated gene that encodes a protein colocalized with synapsin. Eur J Neurosci 2004, 20(3):603-610. 10.1111/j.1460-9568.2004.03473.x, 15255972.
28. Winter S.L, Bosnoyan-Collins L, Pinnaduwage D, Andrulis I.L. The interaction of PP1 with BRCA1 and analysis of their expression in breast tumors. BMC Cancer 2007, 7:85. 10.1186/1471-2407-7-85, 1906825, 17511879.
29. Peri S, Navarro J.D, Kristiansen T.Z, Amanchy R, Surendranath V, Muthusamy B, Gandhi T.K.B, Chandrika K.N, Deshpande N, Suresh S, Rashmi B.P, Shanker K, Padma N, Niranjan V, Harsha H.C, Talreja N, Vrushabendra B.M, Ramya M.A, Yatish A.J, Joy M, Shivashankar H.N, Kavitha M.P, Menezes M, Choudhury D.R, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda C.K, Prasad C.K, Kumar-Sinha C, Deshpande K.S, Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 2004, 32:D497-D501. 10.1093/nar/gkh070, 308804, 14681466.
30. Stark C, Breitkreutz B.J, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, (34 Database):D535-D539. 10.1093/nar/gkj109, 1347471, 16381927.
31. Bader G.D, Donaldson I, Wolting C, Ouellette B.F, Pawson T, Hogue C.W. BIND-The Biomolecular Interaction Network Database. Nucleic Acids Res 2001, 29:242-245. 10.1093/nar/29.1.242, 29820, 11125103.
32. Dobbin K.K, Kawasaki E.S, Petersen D.W, Simon R.M. Characterizing dye bias in microarray experiments. Bioinformatics 2005, 21(10):2430-2437. 10.1093/bioinformatics/bti378, 15774555.
33. Martin-Magniette M, Aubert J, Cabannes E, Daudin J. Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 2005, 21(9):1995-2000. 10.1093/bioinformatics/bti302, 15691855.
34. Zahurak M, Parmigiani G, Yu W, Scharpf R.B, Berman D, Schaeffer E, Shabbeer S, Cope L. Pre-processing Agilent microarray data. BMC Bioinformatics 2007, 8:142. 10.1186/1471-2105-8-142, 1876252, 17472750.
35. Bertucci F, Eisinger F, Tagett R, Sobol H, Birnbaum D. Re: Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J Natl Cancer Inst 2002, 94(19):1506-1507.
36. Rosen E.M, Fan S, Pestell R.G, Goldberg I.D. BRCA1 in hormone-responsive cancers. Trends Endocrinol Metab 2003, 14(8):378-385. 10.1016/j.tem.2003.08.001, 14516936.
37. Woolf P.J, Wang Y. A fuzzy logic approach to analyzing gene expression data. Physiol Genomics 2000, 3:9-15.
38. Li K.C. Genome-wide coexpression dynamics: theory and application. Proc Natl Acad Sci USA 2002, 99(26):16875-16880. 10.1073/pnas.252466999, 139237, 12486219.
39. Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics 2007, 23(21):2903-2909. 10.1093/bioinformatics/btm482, 17921496.
40. Alon U, Barkai N, Notterman D.A, Gish K, Ybarra S, Mack D, Levine A.J. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 1999, 96(12):6745-6750. 10.1073/pnas.96.12.6745, 21986, 10359783.
41. Golub T.R, Slonim D.K, Tamayo P, Huard C, Gaasenbeek M, Mesirov J.P, Coller H, Loh M.L, Downing J.R, Caligiuri M.A, Bloomfield C.D, Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531, 10521349.
42. Pomeroy S.L, T P, Gaasenbeek M, Sturla L.M, A M, McLaughlin M.E, Kim J.Y.H, Goumnerova L.C, Black P.M, Lau C, Allen J.C, Zagzag D, Olson J.M, Curran T, Wetmore C, Biegel J.A, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis D.N, Mesirov J.P, Lander E.S, Golub T.R. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, 415(6870):436-442. 10.1038/415436a, 11807556.
43. Shipp M.A, Ross K.N, Tamayo P, Weng A.P, Kutok J.L, Aguiar R.C.T, Gaasenbeek M, Angelo M, Reich M, Pinkus G.S, Ray T.S, Koval M.A, Last K.W, Norton A, Lister T.A, Mesirov J, Neuberg D.S, Lander E.S, Aster J.C, Golub T.R. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 2002, 8:68-74. 10.1038/nm0102-68, 11786909.
44. Singh D, Febbo P.G, Ross K, Jackson D.G, Manola J, Ladd C, Tamayo P, Renshaw A.A, D'Amico A.V, Richie J.P, Lander E.S, Loda M, Kantoff P.W, Golub T.R, Sellers W.R. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002, 1(2):203-209. 10.1016/S1535-6108(02)00030-2, 12086878.
45. Stuart R.O, Wachsman W, Berry C.C, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S, McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci USA 2004, 101(2):615-620. 10.1073/pnas.2536479100, 327196, 14722351.
46. Welsh J.B, Sapinoso L.M, Su A.I, Kern S.G, Wang-Rodriguez J, Moskaluk C.A, Frierson H.F, Hampton G.M. Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res 2001, 61(16):5974-5978.
47. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang C.H, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov J.P, Poggio T, Gerald W, Loda M, Lander E.S, Golub T.R. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 2001, 98(26):15149-15154. 10.1073/pnas.211566398, 64998, 11742071.