Data analysis from GEO and the TCGA datasets

Data analysis was performed using the NCBI GEO microarray dataset (http://www.ncbi.nlm.nih.gov/geo/) with accession number {"type":"entrez-geo","attrs":{"text":"GSE12777","term_id":"12777"}}GSE12777. Raw microarray data for chemokines were obtained from RNA expression levels in 51 human BC cell lines. The basal chemokine expression levels were determined by global gene expression profiling of BC cell lines, while molecular subtyping was determined using gene expression and HER2 status by fluorescent in situ hybridization. We employed Gitools 2.3.1 (http://www.gitools.org), an open-source tool based on Oracle Java 7, to analyze and visualize the genomic data via interactive heat-maps [82]. The breast invasive carcinoma dataset from TCGA individual projects was used to analyze different BC subtypes (http://www.gitools.org/datasets/tcga).