Open Access Research article

Gene expression profiles of breast biopsies from healthy women identify a group with claudin-low features

Vilde D Haakensen123, Ole Christian Lingjærde45, Torben Lüders6, Margit Riis67, Aleix Prat8, Melissa A Troester9, Marit M Holmen10, Jan Ole Frantzen11, Linda Romundstad12, Dina Navjord13, Ida K Bukholm1427, Tom B Johannesen15, Charles M Perou8, Giske Ursin151617, Vessela N Kristensen126, Anne-Lise Børresen-Dale12 and Åslaug Helland123*

Author Affiliations

1 Dept of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway

2 Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway

3 Dept of Oncology, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway

4 Biomedical Research Group, Department of Informatics, University of Oslo, 0316 Oslo, Norway

5 Center for Cancer Biomedicine, University of Oslo, 0310 Oslo, Norway

6 Department of Clinical Molecular Biology, Division of Medicine and Laboratory Sciences, Institute for Clinical Medicine, Akershus University Hospital, University of Oslo, 0316 Oslo, Norway

7 Dept of Surgery, Akerhus University Hospital, 1478 Lørenskog, Norway

8 Dept of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA

9 Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA

10 Dept of Radiology, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway

11 Dept of Radiology, University Hospital of North Norway, 9038 Tromsø, Norway

12 Dept of Radiology, Buskerud Hospital, 3004 Drammen, Norway

13 Dept of Radiology, Innlandet Hospital, 2609 Lillehammer, Norway

14 Institute of Health Promotion, Akershus University Hospital, 1478 Lørenskog, Norway

15 The Norwegian Cancer Registry, 0304 Oslo, Norway

16 Dept of Nutrition, School of Medicine, 0316 University of Oslo, Oslo, Norway

17 Dept of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA

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BMC Medical Genomics 2011, 4:77  doi:10.1186/1755-8794-4-77

Published: 1 November 2011

Additional files

Additional file 1:

Genelists from the literature. Genelists obtained from different publications describing various breast cells. Reference to each publication and listings of Agilent IDs and gene symbol for all genes included in each list.

Format: XLSX Size: 191KB Download file

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Additional file 2:

Significanc analysis of microarrays (SAM) of cluster 1 vs 2. A file showing input and output from SAM analysis including list of differentially expressed genes with Agilent IDs, gene symbol, scores, fold change and q-values.

Format: XLS Size: 9.1MB Download file

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Additional file 3:

Supplementary material. Table S1: Gene ontology terms enriched in the genes differentially expressed between the two main clusters in the MDG dataset (cluster 1 and 2 in Figure 1) and the AHUS1 dataset (small and large cluster in Figure 2). Table S2: S2 Gene set enrichment analysis (GSEA) of cluster 1 versus cluster 2 using selected gene lists from the literature. Table S3: Comparison of cluster 1 and cell types/subtypes from published gene lists. The number of genes up- and down-regulated is given for genes characterizing each cell type and each cluster. Figure S1: Hierarchical clustering of gene expression of 79 samples from breasts of healthy women. The samples are clustered based on gene lists from the literature, describing different cell types. Figure S2: Biopsies from healthy women (MDG) clustered with two unpublished datasets including mammoplasty reductions and tumor adjacent normal breast tissue. Figure S3: Unsupervised hierarchical clustering of 79 samples from breasts of healthy women. Includes estimated subtype of non-claudin-low samples.

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