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Challenges in projecting clustering results across gene expression-profiling datasetsLusa, Lara ...Background: Gene expression microarray studies for several types of cancer have been reported to identify previously unknown subtypes of tumors. For breast cancer, a molecular classification ... consisting of five subtypes based ongene expression microarray data has been proposed. These subtypes have been reported to exist across several breast cancer microarray studies, and they have demonstrated some association with clinical outcome. A classification rule based on the method of centroids has been proposed for identifying the subtypes in new collections of breast cancer samples; the method is based on the similarity of the new profiles to the mean expression profile of the previously identified subtypes. Methods: Previously identified centroids of five breast cancer subtypes were used to assign 99 breast cancer samples, including a subset of 65 estrogen receptor-positive (ER+) samples, to five breast cancer subtypes based on microarray data for the samples. The effect ofmean centering the genes (i.e., transforming the expression of each gene so that its mean expression is equal to 0) on subtype assignment by method of centroids was assessed. Further studies of the effect of mean centering and of class prevalence in the test set on the accuracy of method of centroids classifications of ER status were carried out using training and test sets forwhich ER status had been independently determined by ligand-binding assay and for which the proportion of ER+ and ER- samples were systematically varied. Results: When all 99 samples were considered, mean centering before application of the method of centroids appeared to be helpful for correctly assigning samples to subtypes, as evidenced by the expression of genes that had previously been used as markers to identify the subtypes. (Abstract truncated at 2000 characters)Vir: Journal of the National Cancer Institute. - ISSN 0027-8874 (Letn. 99, št. 22, 2007, str. 1715-1723)Vrsta gradiva - članek, sestavni delLeto - 2007Jezik - angleškiCOBISS.SI-ID - 23695577
Avtor
Lusa, Lara |
McShane, Lisa M. |
Reid, James F. |
De Cecco, Loris |
Ambrogi, Federico |
Biganzoli, Elia |
Gariboldi, Manuela |
Pierotti, Marco A.
Teme
Breast Neoplasms |
Chemistry |
Genetics |
Cluster Analysis |
Disease-Free Survival |
Gene Expression Regulation, Neoplastic |
Genes, Erbb-2 |
Predictive Value Of Tests |
Receptors, Estrogen |
Analysis |
Genetics |
Research Design |
Tumor Markers, Biological |
Analysis |
Brez bolezni, preživetje |
Dojka, novotvorbe |
Geni erB-2 |
Gensko izražanje, regulacija neoplazemska |
Napovedna vrednost testov |
Raziskava, načrtovanje |
Receptorji estrogenski |
Skupek, analiza |
Tumorski označevalci biološki
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Lusa, Lara | 29917 |
McShane, Lisa M. | ![]() |
Reid, James F. | ![]() |
De Cecco, Loris | ![]() |
Ambrogi, Federico | ![]() |
Biganzoli, Elia | ![]() |
Gariboldi, Manuela | ![]() |
Pierotti, Marco A. | ![]() |
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