Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Solvang, Hiroko K ^a,b   Lingjærde, Ole C ^b   Frigessi, Arnoldo ^b,c   Børresen Dale, Anne Lise ^a,b   Kristensen, Vessela N ^a,d  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c Statistics for Innovation (sfi)2   (Norway)

^d AKERSHUS UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR DEVELOPMENT; COPY NUMBER ABERRATIONS; LINEAR RELATIONSHIPS; NON-LINEAR RELATIONSHIPS; NONLINEAR AMPLIFICATION; NONLINEAR DEPENDENCE; REGULATORY MECHANISM; STATISTICAL APPROACH;

DISEASES; ENZYME KINETICS; GENE EXPRESSION; METABOLISM; NUCLEIC ACIDS; PHYSIOLOGY; REGRESSION ANALYSIS;

GENE EXPRESSION REGULATION;

ALGORITHM; ARTICLE; BREAST TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METABOLISM; PATHOLOGY; SIGNAL TRANSDUCTION;

ALGORITHMS; BREAST NEOPLASMS; COMPARATIVE GENOMIC HYBRIDIZATION; GENE DOSAGE; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

EID: 79956281142     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-197     Document Type: Article

References (21)

1. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Lønning PE, Børresen-Dale AL. Gene expression patterns of breast carcinomas. PNAS 2001, 98:10869-10874. 10.1073/pnas.191367098, 58566, 11553815.
2. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Sshreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536. 10.1038/415530a, 11823860.
3. Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Res 2009, 11:R55. 10.1186/bcr2344, 2750116, 19638211.
4. Chin SF, Teschendroff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biology 2007, 8:R215. 10.1186/gb-2007-8-10-r215, 2246289, 17925008.
5. He M, Rosen J, Mangiameli D, Libutti SK. Cancer development and progression. Adv Exp Med Biol 2007, 593:117-33. 10.1007/978-0-387-39978-2_12, 17265722.
6. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 2002, 1:6240-6245.
7. Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Boststein D, Børresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002, 99:12963-12968. 10.1073/pnas.162471999, 130569, 12297621.
8. Lee H, Kong SW, Park PJ. Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. Bioinformatics 2008, 24:889-896. 10.1093/bioinformatics/btn034, 2600603, 18263644.
9. Witten DM, Tibshirani R, Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 2009, 10:515-534. 10.1093/biostatistics/kxp008, 2697346, 19377034.
10. Natrajan R, Weigelt B, Mackay A, Geyer FC, Grigoriadis A, Tan DSP, Jones C, Lord CJ, Vatcheva R, Rodriguez -Pinilla SM, Palacios J, Ashworth A, Reis-Filho JS. An integrative genomic and transcriptomic analysis reveals molecular pathways and networks regulated by copy number aberrations in basal-like, HER2 and luminal cancers. Breast Cancer Res 2010, 121:575-589.
11. van Wieringen WN, van de Wiel MA. Nonparametric testing for DNA copy number induced differential mRNA gene expression. Biometrics 2009, 65:19-29. 10.1111/j.1541-0420.2008.01052.x, 18479479.
12. Schäfer M, Schwender H, Merk S, Haferlach C, Ickstadt K, Dugas M. Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities. Bioinformatics 2009, 25:3228-3235. 10.1093/bioinformatics/btp592, 19828576.
13. Turner N, Lambros MB, Horlings HM, Pearson A, Sharpe R, Natrajan R, Geyer C, van Kouwehove M, Kreike B, Mackay A, Ashworth A, van de Vijver MJ, Reis-Filho JS. Integrative molecular profiling of triple negative breast cancers identifies amplicon drivers and potential therapeutic targets. Oncogene 2009, 489:1-11.
14. Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D. An integrated approach to uncover drivers of cancer. Cell 2010, 143:1005-1017. 10.1016/j.cell.2010.11.013, 21129771.
15. Chari R, Coef BP, Vucic EA, Lockwood WW, Lam WL. An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Systems Biology 2010, 4:67. 10.1186/1752-0509-4-67, 2880289, 20478067.
16. Bnjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B 1995, 57:289-300.
17. Naume B, Zhao X, Synnestvedt M, Borgen E, Russnes HG, Lingjærde OC, Strømberg M, Wiedswang G, Kvalheim G, Kåresen R, Nesland JM, Børresen-Dale AL, Sørlie T. Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Molecular Oncology 2007, 1:160-171. 10.1016/j.molonc.2007.03.004, 19383292.
18. Peiffer DA, Gunderson KL. SNP-CGH technologies for genomic profiling of LOH and copy number. lab technology 2006, CLI.
19. Lingjærde OC, Baumbusch LO, Liestøl K, Glad IK, Børresen-Dale AL. CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 2005, 21:821-822. 10.1093/bioinformatics/bti113, 15531610.
20. Baumbusch LO, Aarøe J, Johansen FE, Hicks J, Sun H, Bruhn L, Gunderson K, Naume B, Kristensen VN, Liestøl K, Børresen-Dale AL, Lingjærde OC. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics 2008, 9:379. 10.1186/1471-2164-9-379, 2547478, 18691401.
21. Akaike H. A new look at the statistical model identification. IEEE Trans Automat Contrl 1974, AC-19:667-674.