Research article
T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers
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* Corresponding author: Thomas Karn t.karn@em.uni-frankfurt.de
1 Department of Obstetrics and Gynecology, J.W. Goethe-University, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
2 Department of Breast Medical Oncology, The University of Texas M.D. Anderson Cancer Center, PO Box 301439, Houston, TX 77230-1439, USA
3 Department of Obstetrics and Gynecology, University of Muenster, Albert-Schweitzer-Straße 33, Muenster 48149, Germany
4 LMU BioCenter, Ludwig Maximilians University Munich, Grosshaderner Straße 2, Planegg-Martinsried 82152, Germany
5 Department of Pathology, J.W. Goethe-University, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
Breast Cancer Research 2009, 11:R15 doi:10.1186/bcr2234
Published: 9 March 2009Additional files
Additional file 1:
An Excel file containing the microarray expression data of the 569 Affymetrix ProbeSets from the immune-related cluster of the datasets Frankfurt and Frankfurt-2 together with estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status (0 = negative, 1 = positive).
Format: XLS Size: 1.9MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
An Adobe file containing a table that lists the Affymetrix HG-U133A datasets used in the present study, their usage as well as the characteristics of the respective cohorts.
Format: PDF Size: 123KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
An Adobe file containing a figure that presents the expression of all 569 Affymetrix ProbeSets from the immune-related gene cluster in a combined cohort of 1,230 samples to tease out their relationship.
Format: PDF Size: 3.5MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
An Adobe file containing a table that lists all 569 Affymetrix ProbeSets of the immune-system-related gene cluster from Additional data file 3.
Format: PDF Size: 436KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
An Adobe file containing a table that presents the detailed list of the 199 Affymetrix ProbeSets of the immune-system-related metagene clusters and their functional annotation.
Format: PDF Size: 476KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 6:
An Adobe file containing two figures presenting the relationship of the expression of the immune-system-related metagenes with estrogen receptor status, human epidermal growth factor receptor 2 status and the presence of stem-cell like markers in all 1,781 samples from all datasets. Unsupervised clustering analysis of the samples using the immune-related metagenes is presented in Supplemental figure S2a. Scatter plots of the five metagenes representing the major clusters are given in Supplemental figure S2b.
Format: PDF Size: 410KB Download file
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Additional file 7:
An Adobe file containing a table that presents the results from multivariate Cox regression of immune-system-related metagenes in relation to disease-free survival of breast cancer patients (n = 1,263).
Format: PDF Size: 60KB Download file
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Additional file 8:
An Adobe file containing a figure that presents a Kaplan–Meier plot that presents the prognostic value of the IgG metagene in breast cancer patients.
Format: PDF Size: 60KB Download file
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Additional file 9:
An Adobe file containing a figure that presents the relationship of the expression of immune-system-related metagenes and response to neoadjuvant chemotherapy. Pretherapeutic breast cancer samples (n = 198) from patients treated with neoadjuvant chemotherapy were stratified according to the estrogen receptor status of the tumor and were analyzed for expression of IgG and lymphocyte-specific kinase metagenes in a scatter plot.
Format: PDF Size: 150KB Download file
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Additional file 10:
An Adobe file containing a table that presents a list of the tissue and cell line samples from Figure 2. Gene Expression Omnibus database accession numbers of expression data from Su and colleagues [GEO:GSE1133] [31] and a description of the samples from immunological cell types and tissues as ordered in Figure 2 (left to right) are given.
Format: PDF Size: 103KB Download file
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