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. 2006 Dec 20;1(1):e26. doi: 10.1371/journal.pone.0000026

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This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

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(A) Experimental design of microarray analysis.

Oct3/4-overexpressing ES cells differentiate to primitive endoderm and mesoderm, whereas Oct3/4-repressed ES cells differentiate towards Trophectoderm.

(B)(C) K-means clusters of gene expression levels analyzed by TIGR MEV tool (http://www.tigr.org) and their landscape representations by MATLAB.

(D) Comparison of genes grouped in each cluster of ZHTc6 cells and ZHBTc4 cells.

The arrows (red and green) show highly correlated clusters between two cell lines (see Materials and Methods).

(E) Diagram summarizing the unique mode of gene expression regulation by Oct3/4.

Representative Genes identified as the direct downstream targets of Oct3/4 by the ChIP-on-chip assay [33] or ChIP-PET assay [34] are shown. Spp1 and Zfp42 (marked with asterisk) were not detected as a direct downstream target by either ChIP-on-chip or ChIP-PET assays, but have already been shown as such by more direct experimental methods (see the text).