Figure 2

Comparative transcriptome map of human ES and EB on chromosome 17. The transcriptome map shows the coexpression index value of genes displayed according to their positions along the chromosome (horizontal axis). Each dot represents a gene expressed in ES (blue) or EB (red) cells. The yellow line represents the threshold coexpression index (0.3). The coexpression index was calculated as the average Pearson's correlation coefficient between the expression level of a given gene with that of every neighboring gene (10 up- and 10 downstream). The chromosomal position on the horizontal axis is illustrated by both coordinates (mega base pair) and the ideogram with markers of cytogenetic bands [20]. The statistical significance of the coexpression pattern was confirmed by Monte-Carlo simulation (see Methods). A . Transcriptome map constructed with the real genome data, where multiple peaks of coexpression above the threshold are visible and appear as non-random. The co-expressed genes include, from left to right, ORIA1, SOX15, ALDH3A2, PIPOX, KRTHA8, STAT3, COX11, MIRPL38, and PCYT2 (indicated by arrows). B . Transcriptome map by randomized genome data, where peaks of coexpression are random and few are above the threshold.