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Supplemental
Information for:
Gene Expression Profiles in Hereditary Breast Cancer
Ingrid Hedenfalk1,2*, David Duggan1*, Yidong Chen1, Michael Radmacher3, Michael Bittner1, Richard Simon3, Paul Meltzer1, Barry Gusterson4, Manel Esteller5, Mark Raffeld6, Zohar Yakhini7, Amir Ben-Dor7, Edward Dougherty8, Juha Kononen1, Lukas Bubendorf1,9, Wilfrid Fehrle6, Stefania Pittaluga6, Sofia Gruvberger2, Niklas Loman2, Oskar Johannsson2, Håkan Olsson2, Benjamin Wilfond10, Guido Sauter9, Olli-P. Kallioniemi1, Åke Borg2,§ and Jeffrey Trent1,§
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1 Cancer
Genetics Branch, National Human Genome Research Institute, NIH, Bethesda,
Maryland 20892
2 Department of Oncology, University of Lund, Sweden
3 DCTDC, National Cancer Institute, NIH, Bethesda, Maryland
20852
4 Department of Pathology, Western Infirmary, University of
Glasgow, G11 6NT, Scotland, UK
5 Division of Tumor Biology, Johns Hopkins Oncology Center,
Baltimore, MD 21231
6 Department of Pathology, National Cancer Institute, NIH,
Bethesda, Maryland 20850
7 Chemical and Biological Systems Department, Agilent Laboratories,
Palo Alto, CA, 94304
8 Department of Electrical Engineering, Texas A & M University,
College Station, Texas 77843
9 Institute of Pathology, University of Basel, Switzerland
10 Medical Genetics Branch, National Human Genome Research
Institute, NIH, Bethesda, Maryland 20892
*Authors participated
equally/§corresponding author J. Trent (jtrent@nhgri.nih.gov) and Ake Borg (ake.borg@onk.lu.se)
FIGURES & TABLES
Overview
of cDNA Microarray and Tissue Microarray Procedure. Figure
1.jpg
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Identification of Genes Discriminating Distinct Breast Cancer Clusters. Figure 2 .jpg
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- List of 3226 genes
included in statistical analyses after filtering
Download format description
Download Tab-Delimited Text file - List of 51 genes discriminating
BRCA1, BRCA2, and sporadic breast tumors Download
PDF file
- Statistical Methods
(F and t tests) Download PDF file
- 3D animation of MDS
plot Fig. 2B View
quicktime animation
- 3D animation of MDS plot Fig. 2C View quicktime animation
Analysis of Genes Separating BRCA1 Mutation Positive and BRCA2 Mutation Positive Breast Cancers. Figure 3.jpg
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- Consensus list of 176
genes discriminating BRCA1 and BRCA2 breast tumors Download
PDF file
- 3D animation of MDS plot Fig. 3B. View quicktime animation
- Statistical Methods (Weighted Gene Analysis) Download PDF file
- Statistical Methods (Mutual Information and TNoM Analyses) Download PDF file
BRCA1 vs. non-BRCA1 Analyses Download PDF file
BRCA2 vs. non-BRCA2 Analyses Download PDF file
- Extended tissue microarray results and discussion Download PDF file
- Information Abundance by TNoM Scoring TNoM figure.jpg
- 3D animation of MDS plot Fig. 3B. View quicktime animation
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Methylation Analysis of the BRCA1 Promoter in Sporadic Breast Tumors. Figure 4.jpg
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Clinical and Pathological Characteristics of the BRCA1 and BRCA2 Derived Breast Tumors. Table 1.jpg
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- Detailed Clinical and
Pathological Characteristics of BRCA1 and BRCA2 Derived Breast Tumors
Table
3.jpg
- Detailed Clinical and Pathological Characteristics of Sporadic Breast Tumors Table 4.jpg
- Statistical Methods (Test of association) Download PDF file
- Detailed Clinical and Pathological Characteristics of Sporadic Breast Tumors Table 4.jpg
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Gene Expression-Based Classification of Hereditary Breast Cancers. Table 2.jpg
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- Statistical Methods (Class prediction) Download PDF file
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Supplementary information for Javed Khan, et. al, Nature Medicine, 7(6):673-679, 2001. |
The Nature Medicine paper: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks is available here. |
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| NHGRI Homepage Cancer Genetics Branch Tissue Microarrays |