Research article
Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer
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* Corresponding author: Sherene Loi sherene.loi@bordet.be
1 Department of Research, Molecular Oncology Lab, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
2 Translational and Functional Genomics Unit, Jules Bordet Institute, Brussels, Belgium
3 Department of Medicine, St. Vincent Hospital, University of Melbourne, Victoria, Australia
4 Department of Bioinformatics, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
BMC Medical Genomics 2009, 2:37 doi:10.1186/1755-8794-2-37
Published: 24 June 2009Additional files
Additional file 1:
Growth Factor activation/ERBB2 gene set. List of Affymetrix probe sets and annotations used for the growth factor/ERBB2 signaling gene set used in the GSEA.
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Additional file 2:
Table of results generated from Gene Set Enrichment Analysis (GSEA) comparing ER+ BC subtypes. GSEA comparing low and high-risk ER+ BC subtypes as defined by the GGI. 536 gene sets were assessed for enrichment. Cut-off is taken at a nominal p value < 0.05 and a false discovery rate (FDR) < 0.20. ES: enrichment score; Norm ES: nomalized enrichment score; p value: nominal p value; FDR: false discovery rate; Color coded pathways: Grey: cell cycle; Pink: metabolism-related; Red: ERBB2/PI3K/AKT-related; Green: apoptosis-related; Blue: DNA damage pathways. For further information see: http://www.broad.mit.edu/gsea/ webcite
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Additional file 3:
Ingenuity Pathways Analysis of the growth factor/ERBB2 signaling gene set. Growth factor/ERBB2 signaling gene set: molecular network proposed by Ingenuity Pathways Analysis (IPA). Top significant canonical pathways is "Neuregulin signaling" (p = 0.005), top related function is "Cancer" (p = 0.00001). Colored nodes represent genes present in the gene set.
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Additional file 4:
GSEA from MCF-7 cell lines treated with heregulin (HRG). Table showing enrichment results for the MCF-7 cell lines treated with heregulin (HRG).
Format: XLS Size: 16KB Download file
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