Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Czwan, Esteban ^a,b   Brors, Benedikt ^b   Kipling, David ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APICAL PLASMA MEMBRANE; BIOLOGICAL PROCESS; FALSE POSITIVE RATES; FATTY ACID METABOLISM; MICROARRAY DATA SETS; NON-UNIFORM DISTRIBUTION; PERMUTATION APPROACH; RECEPTOR-MEDIATED ENDOCYTOSIS;

CELL MEMBRANES; GENE EXPRESSION; MOLECULAR BIOLOGY; STATISTICAL TESTS;

DISEASES;

TUMOR MARKER;

ARTICLE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METHODOLOGY; NEOPLASM; STATISTICAL DISTRIBUTION; SURVIVAL;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; STATISTICAL DISTRIBUTIONS; SURVIVAL ANALYSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 77349098815     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-19     Document Type: Article

References (31)

1. Liu ET. Mechanism-derived gene expression signatures and predictive biomarkers in clinical oncology. Proc Natl Acad Sci USA 2005, 102:3531-3532. 10.1073/pnas.0500244102, 553302, 15738396.
2. BioCarta. , http://www.biocarta.com/
3. The Gene Ontology Consortium Gene ontology: tool for the unification of biology. Nat Genet 2000, 25(25):25-9. The Gene Ontology Consortium.
4. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 2007, 8:217. 10.1186/1471-2105-8-217, 1924866, 17588266.
5. Kanehisa M. Toward pathway engineering: a new database of genetic and molecular pathways. Sci Technol Japan 1996, 59:5.
6. Ingenuity Systems. , http://www.ingenuity.com/
7. GeneGO. , http://www.genego.com/
8. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, Rijn M, Botstein D, Brown PO. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2004, 2:206-214.
9. Chi JT, Wang Z, Nuyten DS, Rodriguez EH, Schaner ME, Salim A, Wang Y, Kristensen GB, Helland A, Børresen-Dale AL, Giaccia A, Longaker MT, Hastie T, Yang GP, Vijver MJ, Brown PO. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med 2006, 3:395-409.
10. Goeman JJ, Bühlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23:980-987. 10.1093/bioinformatics/btm051, 17303618.
11. Storey JD, Tibshirani R. Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 2003, 100:9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
12. Grate LR. Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery. BMC Bioinformatics 2005, 6:97. 10.1186/1471-2105-6-97, 1090559, 15826317.
13. Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci USA 2009, 106:2824-2828. 10.1073/pnas.0809444106, 2636731,2636731, 19196983.
14. Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, Hofer MD, Mertz KD, Gerstein M, Rubin MA. Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Res 2007, 67:10296-10303. 10.1158/0008-5472.CAN-07-2173, 17974971.
15. Lu X, Perkins DL. Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures. BMC Bioinformatics 2007, 8:157. 10.1186/1471-2105-8-157, 1890303, 17509157.
16. Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008, 9(Suppl 9):S10. 10.1186/1471-2105-9-S9-S10, 2537561, 18793455.
17. Pitroda SP, Khodarev NN, Beckett MA, Kufe DW, Weichselbaum RR. MUC1-induced alterations in a lipid metabolic gene network predict response to human breast cancers to tamoxifen treatment. Proc Natl Acad Sci USA 2009, 106:5837-5841. 10.1073/pnas.0812029106, 2656554,2656554, 19289846.
18. Montel V, Gaultier A, Lester RD, Campana WM, Gonias SL. The Low-Density Lipoprotein Receptor-Related Protein Regulates Cancer Cell Survival and Metastasis Development. Cancer Res 2007, 67:9817-9824. 10.1158/0008-5472.CAN-07-0683, 17942912.
19. Papadimitrakopoulou V, Adjei AA. The Akt/mTOR and mitogen-activated protein kinase pathways in lung cancer therapy. J Thorac Oncol 2006, 1(1):749-51.
20. Haluska FG, Ibrahim N. Therapeutic targets in melanoma: map kinase pathway. Curr Oncol Rep 2006, 8(8):400-5. 10.1007/s11912-006-0065-x, 16901402.
21. Milella M, Kornblau SM, Andreeff M. The mitogen-activated protein kinase signaling module as a therapeutic target in hematologic malignancies. Rev Clin Exp Hematol 2003, 7(7):160-90.
22. Vlahakis NE, Schroeder MA, Pagano RE, Hubmayr RD. Role of deformation-induced lipid trafficking in the prevention of plasma membrane stress failure. Am J Respir Crit Care Med 2002, 166(166):1282-1289. 10.1164/rccm.200203-207OC, 12403699.
23. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lønning P, Børresen-Dale AL. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874. 10.1073/pnas.191367098, 58566, 11553815.
24. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, (35 Database):D766-770. 10.1093/nar/gkl1019, 1781111, 17182626.
25. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 2001, 98:13784-13789. 10.1073/pnas.241500798, 61119, 11707590.
26. The Cancer Genome Anatomy Project. , http://cgap.nci.nih.gov/
27. Alibés A, Yankilevich P, Cañada A, Díaz-Uriarte R. IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC Bioinformatics 2007, 8:9. 10.1186/1471-2105-8-9, 1779800, 17214880.
28. R Development Core Team R: A language and environment for statistical computing 2008, Vienna: R Foundation for Statistical Computing, Vienna, R Development Core Team.
29. Hothorn T, Lausen B. On the exact distribution of maximally selected rank statistics. Computational Statistics & Data Analysis 2003, 43:121-137.
30. Turner FS, Clutterbuck DR, Semple CA. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol 2003, 4:R75. 10.1186/gb-2003-4-11-r75, 329128, 14611661.
31. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 1995, 57:289-300.