Delineation of Oct3/4-downstream target gene network.

<div><p>(A) A list of genes that have been experimentally demonstrated as the direct downstream targets of Oct3/4.</p> <p>Yes: genes that were also detected by the global ChIP assays.</p> <p>No: genes that were not detected by the global ChIP assays.</p> <p>Mouse homologues of human genes identified in Boyer <i>et al</i>. were generated using NCBI HomoloGene Build 49.</p> <p>(B) Comparison of gene lists obtained by the expression profiling (list 1 plus list 2) and global ChIP assays.</p></div

Principal component analysis (PCA) and the expression pattern heatmap of known target genes for Oct3/4 and related genes.

<div><p>(A) 2D-views of PCA for 2,757 genes that were identified as significantly differentially expressed during this time course.</p> <p>(B) The expression pattern and ES/TS specificity of each component of PCA was classified into 4 groups (Group I ∼ Group IV).</p> <p>(C) Known target genes for Oct3/4 and related genes.</p> <p>(D) Top 30 up- and down-regulated genes from 0 h v 24 h.</p></div

<b>Functional analysis of Tcl1 in ES cells</b>.

<div><p>(A) Expression level of Tcl1 gene effects on cell proliferation.</p> <p>The number of ES cells decreased when Tcl1 was knocked down by shRNA.</p> <p>(B) RT-PCR and Western blot analysis of ES cells with shRNA of Tcl1 gene.</p> <p>Tcl1 gene expression affected active Akt1 (p-Ser.473 Akt1), but not wild type of Akt1.</p> <p>(C) Reversibility of Tcl1 downregulation effect.</p> <p>The number of cells was rescued in the absence of Tet.</p> <p>(D) Photomicrographs of ES cell cultures.</p> <p>The number of ES cells decreased when Tcl1 was knocked down by shRNA.</p> <p>Cell proliferation was rescued in the absence of Tet.</p> <p>(E) Overexpression of Tcl1 does not rescue cell proliferation while Oct3/4 is repressed.</p> <p>(F) A model for the involvement of Oct3/4-Tcl1-Akt in ES cell proliferation.</p></div

Examples of tentative target genes responding differentially to the suppression of , , and

<p><b>Copyright information:</b></p><p>Taken from "Identification of , , and downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data"</p><p>http://www.biomedcentral.com/1471-2164/9/269</p><p>BMC Genomics 2008;9():269-269.</p><p>Published online 3 Jun 2008</p><p>PMCID:PMC2424064.</p><p></p

Time and magnitude of responses were estimated from the time course microarray data using 1

5-fold expression changes as a threshold (C), and then used as coordinates in a scatter-plot. Tentative target genes were identified as shown in Fig 1.<p><b>Copyright information:</b></p><p>Taken from "Identification of , , and downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data"</p><p>http://www.biomedcentral.com/1471-2164/9/269</p><p>BMC Genomics 2008;9():269-269.</p><p>Published online 3 Jun 2008</p><p>PMCID:PMC2424064.</p><p></p