Figure 5.

Comparison of tentative target genes (TTGs) responding to the suppression of Pou5f1, Sox2, or Nanog. (A) Venn diagram of combined TTGs of POU5F1, SOX2, and NANOG. Number of genes that were up-regulated (magenta), down-regulated (blue), or had a mixed response (gray) to the suppression of Pou5f1, Sox2, and Nanog. (B) The same Venn diagram as (A) after removing genes with possible indirect effects. (C) Comparison of gene responses to the suppression of Pou5f1 and Sox2 (TTGs of POU5F1 that were down-regulated after Pou5f1 suppression): response time ratio = log10(t2/t1) where t1 and t2 are response times to Pou5f1 and Sox2 suppression, respectively; difference of response magnitude = m2 - m1, where m1 and m2 are response magnitudes (log-ratios) to Pou5f1 and Sox2 suppression, respectively; genes in the blue quadrant responded more strongly and faster to Sox2 suppression than to Pou5f1 suppression, and genes in the yellow quadrant responded more strongly and faster to Pou5f1 suppression than to Sox2 suppression. (D) Comparison of gene responses to the suppression of Pou5f1 and Nanog (TTGs of Pou5f1 that were down-regulated after Pou5f1 suppression); notations are the same as in (C).

Sharov et al. BMC Genomics 2008 9:269   doi:10.1186/1471-2164-9-269
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