Figure 2

Representation of gene signatures across BC cell lines. BC cell lines are ranked based on their gene expression clustering. (A) Expression levels of eleven gene signatures previously associated with ER-negative BC. Similarities between gene signature and each BC cell line transcriptome was established as described in Material and Methods, and used for ranking lines. Each coloured square represents the rank (between 1 and 25) of the cell line to the specific gene signature, whereby blue indicates the highest rank (best resemblance to the gene signature), while white being the lowest rank. Gene signatures used were: G3.TN.Tumour [43]; Apocrine.Basal [9]; Interferon [28]; IGF1 [39]; EGFR [41]; c-MET [42]; Mammosphere [40]; CD24.CD44 [44]; HighGradeVLowGrade [47]; GGI [68]; Stroma [45]. (B) Classification of BC cell lines to BC subtypes by nearest centroid correlation based on gene expression signatures: PAM50 [26]; Sorlie500 [27]; Hu306 [69]; Claudin.Low [8], Teschendorff.ER.neg [25]; CIT256 [10]; both subtype assignment and Spearman correlation are presented.