ERposAge

Supplementary Resource to:

Qing T, Karn T et al. Molecular differences between younger versus older ER-positive and HER2-negative breast cancers. npj Breast Cancer. 2022 Nov 7;8(1):119. doi: 10.1038/s41523-022-00492-0

PMID 36344517

https://www.ncbi.nlm.nih.gov/pubmed/36344517/

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This resource contains the following data regarding the analyses described in the paper:

Directory Microarray contains data related to Affymetrix microarray analyses in the paper:

1. Affymetrix_Analyses.Rmd: An R-Markdown file of the Affymetrix analyses in the paper

2. Affymetrix_Analyses.html: The corresponding code together with all output from Affymetrix_Analyses.Rmd

3. Sudirectory data with the following input files for the R-Markdown script:

• n2007_SampleInfo.txt
• signatures.txt
• Common39Genes-probesets.txt

4. Affymetrix_Analyses.zip: A zip package for downloading all files above (1.-3.):

NOTE:

One additional file necessary for the microarray analysis is NOT available in this resource due to size:

• The file n2007_MAS5.txt contains all Affymetrix microarray data and can be downloaded as a 187 MB zip file from: https://user.uni-frankfurt.de/~tkarn/data/n2007_MAS5.zip

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Directory METABRIC contains data related to METABRIC analyses in the paper:

1. METABRIC_Analyses.Rmd: An R-Markdown file of the METABRIC analyses in the paper

2. METABRIC_Analyses.html: The corresponding code together with all output from METABRIC_Analyses.Rmd

3. sudirectory data with the following input files for the R-Markdown script:

• data_clinical.txt
• signatures.txt
• Common39Genes-probesets.txt

4. sudirectory functions with the R-script:

• oncotypedx2_withoutBAG1.R (an adapted oncotypedx function from the genefu package leaving out the gene BAG1, which is not available in METABRIC expression data)

5. METABRIC_Analyses.zip: A zip package for downloading all files above (1.-4.):

NOTE:

One additional file necessary for the METABRIC analysis is NOT available in this resource due to size:

• The log expression data and clinical data for 1980 breast cancer samples can be downloaded from cBioPortal or as a zip file from: https://user.uni-frankfurt.de/~tkarn/data/METABRIC.zip