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. 2011 Mar 15;104(6):971–981. doi: 10.1038/bjc.2011.66

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Copyright © 2011 Cancer Research UK

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Unsupervised clustering of 1000 probesets with the highest variance across the 28 FFPE cervical cancer samples. (A) Each row represents a probeset; each column represents a sample. The expression level of each probeset was standardised by subtracting that probeset's mean expression from its expression value and then dividing by the standard deviation across all the samples. This scaled expression value, denoted as the row Z-score, is plotted in red–blue colour scale with red indicating high expression and blue indicating low expression. Hierarchical clustering of genes and samples was based on Pearson's correlation. The first colour bar at the top indicates the histological classifications of the samples: SCC in orange and AC in green. p63 staining status is indicated by the second coloured bar, where black represents p63+ and white represents p63−. (B) Principal component analysis of the top 1000 most variable probesets. Different colours are used for the two histological subtypes: orange represents SCC samples; green represent AC samples. (C) Percentage variance explained by the first 10 principal components.