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We thank present and former members of the Breast Cancer Outcomes Unit and Genetic Pathology Evaluation Centre for assembly of the tissue microarray series and clinical database.
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Microarray series data and corresponding platform annotations from DR/fasting experiments were downloaded from the Gene Expression Omnibus at http://www.ncbi.nlm.nih.gov/geo/.nih.gov/geo/
For each microarray series, all normalization steps including intra-series and inter-series normalization, correction of intensity values to the total RNA quantity and their centering reduction were as previously described [ 18].
We downloaded Affymetrix microarray series GSE32426 consisting of rice embryogenic calli before and after Agrobacterium infection from NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/) (Tie et al. 2012).
To explore to what extent the protein level was reflected in mRNA expression, GPER gene expression data were investigated in 76 tumour specimens analysed by microarray and validated by qPCR in 161 patients independent from the microarray series.
For this purpose, we performed hierarchical clustering in a previously published large microarray series of primary breast cancer patients (n = 850) with availability of distant metastases-free survival data (DMFS) [41].
In the present study, we re-analyzed these microarray series focusing on the prophage-like regions.
These microarray series were re-analyzed with the focus on the prophage-like regions (Table 3).
Data from this microarray series has been deposited in GEO under accession number GSE6855.
Biopsy 242-NT (non-neoplastic tissue) was not included in the original microarray series [ 20].
For each microarray series, intra-series normalization to correct experimental variations after fraction collection was performed using a common reference.
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