{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T12:58:59Z","timestamp":1761742739107,"version":"3.32.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: In recent years, microarray technology has revealed many tumor-expressed genes prognostic of clinical outcomes in early-stage breast cancer patients. However, in the presence of cured patients, evaluating gene effect on time to relapse is quite complex since it may affect either the probability of never experiencing a relapse (cure effect) or the time to relapse among the uncured patients (disease progression effect) or both. In this context, we propose a simple and an efficient method for identifying gene expression changes that characterize early and late recurrence for uncured patients.<\/jats:p><jats:p>Results: Simulation results show the good performance of the proposed statistic for detecting a disease progression effect. In a study of early-stage breast cancer, our results show that the proposed statistic provides a more powerful basis for gene selection than the classical Cox model-based statistic. From a biological perspective, many of the genes identified here as associated with the speed of disease recurrence have known roles in tumorigenesis.<\/jats:p><jats:p>Contact: \u00a0broet@vjf.inserm.fr; kuznetsov@gis.a-star.edu.sg<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl110","type":"journal-article","created":{"date-parts":[[2006,3,22]],"date-time":"2006-03-22T02:33:29Z","timestamp":1142994809000},"page":"1477-1485","source":"Crossref","is-referenced-by-count":23,"title":["Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients"],"prefix":"10.1093","volume":"22","author":[{"given":"Philippe","family":"Bro\u00ebt","sequence":"first","affiliation":[{"name":"Facult\u00e9 de M\u00e9decine\u2014Universit\u00e9 1 \u00a0 1 \u00a0 \u00a0 Paris-XI, IFR69, 16 Avenue Paul Vaillant Couturier 94807 Villejuif Cedex, France"}]},{"given":"Vladimir A.","family":"Kuznetsov","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore 2 \u00a0 2 \u00a0 \u00a0 60 Biopolis Street, Singapore 138672, Singapore"}]},{"given":"Jonas","family":"Bergh","sequence":"additional","affiliation":[{"name":"Department of Oncology and Pathology, Radiumhemmet, Karolinska Institute and Hospital 3 \u00a0 3 \u00a0 \u00a0 S-171 76 Stockholm, Sweden"}]},{"given":"Edison T.","family":"Liu","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore 2 \u00a0 2 \u00a0 \u00a0 60 Biopolis Street, Singapore 138672, Singapore"}]},{"given":"Lance D.","family":"Miller","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore 2 \u00a0 2 \u00a0 \u00a0 60 Biopolis Street, Singapore 138672, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2006,3,21]]},"reference":[{"key":"2023012408400632400_b1","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/nm733","article-title":"Gene-expression profiles predict survival of patients with lung adenocarcinoma","volume":"8","author":"Beer","year":"2002","journal-title":"Nat. Med."},{"key":"2023012408400632400_b2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate : a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Statist. Soc. Ser. B"},{"key":"2023012408400632400_b3","volume-title":"The Breast: Comprehensive Management of Benign and Maligant Diseases","author":"Bland","year":"1998","edition":"2nd edn."},{"key":"2023012408400632400_b4","first-page":"216","article-title":"Contribution to the discussion on the paper by D.R. Cox Regression and life tables","volume":"34","author":"Breslow","year":"1972","journal-title":"J. R. Statist. Soc., Ser. B"},{"key":"2023012408400632400_b5","doi-asserted-by":"crossref","first-page":"89","DOI":"10.2307\/2529620","article-title":"Covariance analysis of censored survival data","volume":"30","author":"Breslow","year":"1974","journal-title":"Biometrics"},{"key":"2023012408400632400_b6","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1111\/j.0006-341X.2001.00844.x","article-title":"A semi-parametric approach for the two-sample comparison of survival times with long-term survivors","volume":"57","author":"Bro\u00ebt","year":"2001","journal-title":"Biometrics"},{"key":"2023012408400632400_b7","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1080\/01621459.1979.10481038","article-title":"Robust locally weighted regression and smoothing scatterplots","volume":"74","author":"Cleveland","year":"1979","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012408400632400_b8","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.2517-6161.1972.tb00899.x","article-title":"Regression models and life tables (with Discussion)","volume":"34","author":"Cox","year":"1972","journal-title":"J. R. Statist. Soc. Ser. B"},{"key":"2023012408400632400_b9","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1093\/biomet\/62.2.269","article-title":"Partial likelihood","volume":"62","author":"Cox","year":"1975","journal-title":"Biometrics"},{"key":"2023012408400632400_b10","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-2887-0","volume-title":"Theoretical Statistics","author":"Cox","year":"1974"},{"key":"2023012408400632400_b11","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1093\/bioinformatics\/bti063","article-title":"A simple procedure for estimating the false discovery rate","volume":"21","author":"Dalmasso","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408400632400_b12","first-page":"930","article-title":"Polychemotherapy for early breast cancer: an overview of the randomised trials","volume-title":"Lancet","author":"EBCTCG: Early Breast Cancer Trialists' Collaborative Group.","year":"1998"},{"key":"2023012408400632400_b13","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1365-2559.1991.tb00229.x","article-title":"Pathological prognostic factors in breast cancer. The value of histological grade in breast cancer: experience from a large study with long-term follow-up","volume":"19","author":"Elston","year":"1991","journal-title":"Histopathology"},{"key":"2023012408400632400_b14","doi-asserted-by":"crossref","first-page":"36","DOI":"10.4161\/cbt.3.1.561","article-title":"Wnt signaling and breast cancer","volume":"3","author":"Howe","year":"2004","journal-title":"Cancer Biol. Ther."},{"key":"2023012408400632400_b15","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1002\/path.1475","article-title":"In lymph node-negative invasive breast carcinomas, specific chromosomal aberrations are strongly associated with high mitotic activity and predict outcome more accurately than grade, tumour diameter, and oestrogen receptor","volume":"201","author":"Janssen","year":"2003","journal-title":"J. Pathol."},{"volume-title":"Survival Analysis with Long-Term Survivors","year":"1996","author":"Maller","key":"2023012408400632400_b16"},{"volume-title":"Analysing Survival Data from Clinical Trials and Observation Studies","year":"2004","author":"Marubini","key":"2023012408400632400_b17"},{"key":"2023012408400632400_b18","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1093\/nar\/gki078","article-title":"The PANTHER database of protein families, subfamilies, functions and pathways","volume":"33","author":"Mi","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408400632400_b19","doi-asserted-by":"crossref","first-page":"13550","DOI":"10.1073\/pnas.0506230102","article-title":"An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival","volume":"102","author":"Miller","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"volume-title":"Design and Analysis of DNA Microarray Investigations","year":"2004","author":"Simon","key":"2023012408400632400_b20"},{"key":"2023012408400632400_b21","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1198\/01622145030000001007","article-title":"Estimating cure rates from survival data: an alternative to two-component mixture models","volume":"98","author":"Tsodikov","year":"2003","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012408400632400_b22","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/415530a","article-title":"Gene expression profiling predicts clinical outcome of breast cancer","volume":"415","author":"van t Veer","year":"2002","journal-title":"Nature"},{"key":"2023012408400632400_b23","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1056\/NEJMoa021967","article-title":"A gene-expression signature as a predictor of survival in breast cancer","volume":"347","author":"van de Vijver","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"2023012408400632400_b24","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/S0140-6736(05)17947-1","article-title":"Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer","volume":"365","author":"Wang","year":"2005","journal-title":"Lancet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/12\/1477\/48837983\/bioinformatics_22_12_1477.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/12\/1477\/48837983\/bioinformatics_22_12_1477.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T03:13:49Z","timestamp":1736306029000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/12\/1477\/207108"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,21]]},"references-count":24,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2006,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl110","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2006,6,15]]},"published":{"date-parts":[[2006,3,21]]}}}