Transcriptome heterogeneity of tumors. (A) Six independent microarray experiments, including one normal tissue (Normal) and five tumor collections (HCC1, HCC2, tumor1, tumor2, and tumor3), were compared. The transcriptomic heterogeneity of each sample type was measured by the average of Pearson dissimilarity between paired samples. The heterogeneity of HCCs, even at the most initial stage, appeared to be significantly higher than those of normal livers (p = 1.73E-5, **) and pre-cancers (p = 3.38E-9, ***). Four data sets used for later analyses are marked (¤: Sts, §Sci, #: Sve and ‡: Sva), respectively. (B) The MDS plot of the normal liver and three different liver pathological sample sets. Both very early HCC (green circle) and very advanced HCC samples (red circle) show an obviously wider distribution than normal liver (open circle) and cirrhosis samples (blue circle). (C) The MDS plot of St s data set. Liver and spleen samples are labeled with opened and filled circle respectively.