Herschkowitz, Jason I, He, Xiaping, Fan, Cheng, Perou, Charles M
Abstract Introduction Breast cancers can be classified using whole genome expression into distinct subtypes that show differences in prognosis. One of these groups, the basal-like subtype, is poorly...
Correction: Statistical modeling for selecting housekeeper genes (2008)
Szabo, Aniko, Perou, Charles M, Karaca, Mehmet, Perreard, Laurent, Palais, Robert, Quackenbush, John F, ...
No abstract available.
Wright, Mollie H, Robles, Ana I, Herschkowitz, Jason I, Hollingshead, Melinda G, Anver, Miriam R, Perou, Charles M, ...
Abstract Background Development of therapies for patients with BRCA1 mutations has been hampered by lack of readily available in vitro and in vivo models. We recently showed that transplantation of...
EGFR associated expression profiles vary with breast tumor subtype (2007)
Hoadley, Katherine A, Weigman, Victor J, Fan, Cheng, Sawyer, Lynda R, He, Xiaping, Troester, Melissa A, ...
Abstract Background The epidermal growth factor receptor (EGFR/HER1) and its downstream signaling events are important for regulating cell growth and behavior in many epithelial tumors types. In...
Herschkowitz, Jason I, Simin, Karl, Weigman, Victor J, Mikaelian, Igor, Usary, Jerry, Hu, Zhiyuan, ...
Abstract Background Although numerous mouse models of breast carcinomas have been developed, we do not know the extent to which any faithfully represent clinically significant human phenotypes. To...
Chanock, Stephen J, Burdett, Laurie, Yeager, Meredith, Llaca, Victor, Langerød, Anita, Presswalla, Shafaq, ...
Abstract Introduction Genomic alterations have been observed in breast carcinomas that affect the capacity of cells to regulate proliferation, signaling, and metastasis. Re-sequence studies have...
Gene expression patterns associated with p53 status in breast cancer (2006)
Troester, Melissa A, Herschkowitz, Jason I, Oh, Daniel S, He, Xiaping, Hoadley, Katherine A, Barbier, Claire S, ...
Abstract Background Breast cancer subtypes identified in genomic studies have different underlying genetic defects. Mutations in the tumor suppressor p53 occur more frequently in estrogen receptor...
David S. Shames, Luc Girard, Boning Gao, Mitsuo Sato, Cheryl M. Lewis, Narayan Shivapurkar, ...
BackgroundPromoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated...
The molecular portraits of breast tumors are conserved across microarray platforms (2006)
Hu, Zhiyuan, Fan, Cheng, Oh, Daniel S, Marron, JS, He, Xiaping, Qaqish, Bahjat F, ...
Abstract Background Validation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification....
The molecular portraits of breast tumors are conserved acress microarray platforms (2006)
Hu, Zhiyuan, Fan, Cheng, Oh, Daniel S., Marron, J. S., He, Xiaping, Qaqish, Bahjat F., ...
BackgroundValidation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification. However,...
Perreard, Laurent, Fan, Cheng, Quackenbush, John F, Mullins, Michael, Gauthier, Nicholas P, Nelson, Edward, ...
Abstract Introduction Predicting the clinical course of breast cancer is often difficult because it is a diverse disease comprised of many biological subtypes. Gene expression profiling by microarray...
Statistical modeling for selecting housekeeper genes (2004)
Szabo, Aniko, Perou, Charles M, Karaca, Mehmet, Perreard, Laurent, Quackenbush, John F, Bernard, Philip S
Abstract There is a need for statistical methods to identify genes that have minimal variation in expression across a variety of experimental conditions. These 'housekeeper' genes are widely employed...
Universal Reference RNA as a standard for microarray experiments (2004)
Novoradovskaya, Natalia, Whitfield, Michael L, Basehore, Lee S, Novoradovsky, Alexey, Pesich, Robert, Usary, Jerry, ...
Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a...
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
Perou, Charles M., Jeffrey, Stefanie S., Van De Rijn, Matt, Rees, Christian A., Eisen, Michael B., Ross, Douglas T., ...
cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of...
Sørlie, Therese, Perou, Charles M., Tibshirani, Robert, Aas, Turid, Geisler, Stephanie, Johnsen, Hilde, ...
The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A...
Diversity of gene expression in adenocarcinoma of the lung
Garber, Mitchell E., Troyanskaya, Olga G., Schluens, Karsten, Petersen, Simone, Thaesler, Zsuzsanna, Pacyna-Gengelbach, Manuela, ...
The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression...
Whitfield, Michael L., Sherlock, Gavin, Saldanha, Alok J., Murray, John I., Ball, Catherine A., Alexander, Karen E., ...
The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic...
Pollack, Jonathan R., Sørlie, Therese, Perou, Charles M., Rees, Christian A., Jeffrey, Stefanie S., Lonning, Per E., ...
Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH)...
Repeated observation of breast tumor subtypes in independent gene expression data sets
Sørlie, Therese, Tibshirani, Robert, Parker, Joel, Hastie, Trevor, Marron, J. S., Nobel, Andrew, ...
Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined...
Universal Reference RNA as a standard for microarray experiments
Novoradovskaya, Natalia, Whitfield, Michael L, Basehore, Lee S, Novoradovsky, Alexey, Pesich, Robert, Usary, Jerry, ...
Statistical modeling for selecting housekeeper genes
Szabo, Aniko, Perou, Charles M, Karaca, Mehmet, Perreard, Laurent, Quackenbush, John F, Bernard, Philip S
Statistical models are presented for selecting the best housekeepers to normalize quantitative data within a given tissue type and across different types of tissue samples.
Troester, Melissa A., Hoadley, Katherine A., Parker, Joel S., Perou, Charles M.
Global gene expression profiling has demonstrated that the predominant cellular response to a range of toxicants is a general stress response. This stereotyped environmental stress response commonly...
αB-Crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer
Moyano, Jose V., Evans, Joseph R., Chen, Feng, Lu, Meiling, Werner, Michael E., Yehiely, Fruma, ...
Recent gene profiling studies have identified a new breast cancer subtype, the basal-like group, which expresses genes characteristic of basal epithelial cells and is associated with poor clinical...
The molecular portraits of breast tumors are conserved across microarray platforms
Hu, Zhiyuan, Fan, Cheng, Oh, Daniel S, Marron, JS, He, Xiaping, Qaqish, Bahjat F, ...
Perreard, Laurent, Fan, Cheng, Quackenbush, John F, Mullins, Michael, Gauthier, Nicholas P, Nelson, Edward, ...
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
Perou, Charles M., Jeffrey, Stefanie S., Van De Rijn, Matt, Rees, Christian A., Eisen, Michael B., Ross, Douglas T., ...
cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of...
Sørlie, Therese, Perou, Charles M., Tibshirani, Robert, Aas, Turid, Geisler, Stephanie, Johnsen, Hilde, ...
The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A...
Diversity of gene expression in adenocarcinoma of the lung
Garber, Mitchell E., Troyanskaya, Olga G., Schluens, Karsten, Petersen, Simone, Thaesler, Zsuzsanna, Pacyna-Gengelbach, Manuela, ...
The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression...
Whitfield, Michael L., Sherlock, Gavin, Saldanha, Alok J., Murray, John I., Ball, Catherine A., Alexander, Karen E., ...
The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic...
Pollack, Jonathan R., Sørlie, Therese, Perou, Charles M., Rees, Christian A., Jeffrey, Stefanie S., Lonning, Per E., ...
Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH)...
Repeated observation of breast tumor subtypes in independent gene expression data sets
Sørlie, Therese, Tibshirani, Robert, Parker, Joel, Hastie, Trevor, Marron, J. S., Nobel, Andrew, ...
Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined...
Universal Reference RNA as a standard for microarray experiments
Novoradovskaya, Natalia, Whitfield, Michael L, Basehore, Lee S, Novoradovsky, Alexey, Pesich, Robert, Usary, Jerry, ...
Statistical modeling for selecting housekeeper genes
Szabo, Aniko, Perou, Charles M, Karaca, Mehmet, Perreard, Laurent, Quackenbush, John F, Bernard, Philip S
Statistical models are presented for selecting the best housekeepers to normalize quantitative data within a given tissue type and across different types of tissue samples.
Troester, Melissa A., Hoadley, Katherine A., Parker, Joel S., Perou, Charles M.
Global gene expression profiling has demonstrated that the predominant cellular response to a range of toxicants is a general stress response. This stereotyped environmental stress response commonly...
αB-Crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer
Moyano, Jose V., Evans, Joseph R., Chen, Feng, Lu, Meiling, Werner, Michael E., Yehiely, Fruma, ...
Recent gene profiling studies have identified a new breast cancer subtype, the basal-like group, which expresses genes characteristic of basal epithelial cells and is associated with poor clinical...
The molecular portraits of breast tumors are conserved across microarray platforms
Hu, Zhiyuan, Fan, Cheng, Oh, Daniel S, Marron, JS, He, Xiaping, Qaqish, Bahjat F, ...
Perreard, Laurent, Fan, Cheng, Quackenbush, John F, Mullins, Michael, Gauthier, Nicholas P, Nelson, Edward, ...
Shames, David S, Girard, Luc, Gao, Boning, Sato, Mitsuo, Lewis, Cheryl M, Shivapurkar, Narayan, ...
John Minna and colleagues report that a group of genes are commonly methylated in primary lung, breast, colon, and prostate cancer.
Gene expression patterns associated with p53 status in breast cancer
Troester, Melissa A, Herschkowitz, Jason I, Oh, Daniel S, He, Xiaping, Hoadley, Katherine A, Barbier, Claire S, ...
Chanock, Stephen J, Burdett, Laurie, Yeager, Meredith, Llaca, Victor, Langerød, Anita, Presswalla, Shafaq, ...
Van De Rijn, Matt, Perou, Charles M., Tibshirani, Rob, Haas, Phillippe, Kallioniemi, Olli, Kononen, Juha, ...
While several prognostic factors have been identified in breast carcinoma, the clinical outcome remains hard to predict for individual patients. Better predictive markers are needed to help guide...
Herschkowitz, Jason I, Simin, Karl, Weigman, Victor J, Mikaelian, Igor, Usary, Jerry, Hu, Zhiyuan, ...
Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human...
EGFR associated expression profiles vary with breast tumor subtype
Hoadley, Katherine A, Weigman, Victor J, Fan, Cheng, Sawyer, Lynda R, He, Xiaping, Troester, Melissa A, ...
Molecular analysis reveals heterogeneity of mouse mammary tumors conditionally mutant for Brca1
Wright, Mollie H, Robles, Ana I, Herschkowitz, Jason I, Hollingshead, Melinda G, Anver, Miriam R, Perou, Charles M, ...
Correction: Statistical modeling for selecting housekeeper genes
Szabo, Aniko, Perou, Charles M, Karaca, Mehmet, Perreard, Laurent, Palais, Robert, Quackenbush, John F, ...
A correction to Statistical modeling for selecting housekeeper genes by Aniko Szabo, Charles M Perou, Mehmet Karaca, Laurent Perreard, John F Quackenbush, and Philip S Bernard. Genome Biology 2004,...
Molecular Characterization of Human Breast Tumor Vascular Cells
Bhati, Rajendra, Patterson, Cam, Livasy, Chad A., Fan, Cheng, Ketelsen, David, Hu, Zhiyuan, ...
A detailed understanding of the assortment of genes that are expressed in breast tumor vessels is needed to facilitate the development of novel, molecularly targeted anti-angiogenic agents for breast...