Figure 3

Association scores and expression profiles with genes aligned between (a) and (b). (a) Association scores of the ES genes that are in the uniformly-high cluster, the Oct4 cluster, the Myc cluster, and the Oct4-moderate cluster, with cyan-colored horizontal lines indicating boundaries between the clusters. (b) Gene expression profiles with the first 8 conditions corresponding to ES stage and the rest corresponding to DF stage, annotated by the number of ES-up (indicated by "up") genes and ES-down ("down") genes in each cluster. Note that genes within a cluster are sorted according to their expression fold change. Association scores and gene expression profiles are the same as the ones generated in their original papers. Specifically, the association scores are log-transformed and quantile-normalized [14]; the gene expression profiles in [16] are normalized by the invariant set method implemented by dChip [37]. For display purpose, both the association scores and the gene expression profiles are rescaled to the range between -2 and 2.