Gene Ontology of functional comparison between TS, IVVPS, and IVTPS.

<p>GO slim GOA analysis of the three ontologies are represented separately: (<b>A</b>) Molecular Functions (MF); (<b>B</b>) Biological Process (BP); and (<b>C</b>) Cellular Components (CC). Each GO term from a GOslim subset is represented on the x-axis, and gene content in percentage related to each gene signature is compared on the y-axis. The asterisk marks the over-represented significant terms (GOSlim GOA adjusted-p-value <0.05) in gene signatures after Fisher exact test genome comparison.</p

Experimental design of the study (A).

<p>Differential gene expression profile was carried out in single blastomeres from day-3 embryos, ICM from blastocysts, and their derived hESC counterparts. <b>Principal component analysis (PCA) of the whole transcriptome of single blastomeres from day-3 embryos, ICMs from blastocysts, and hESCs derived from both sources (B) and PCA of the UNS of blastomeres, ICMs, and hESCs (C).</b> Samples in the same cluster category stay closer together than in any other sample. The most separate clusters are blastomeres and hESCs, and ICMs show an intermediate pattern which falls between both. ICM_origin and B_origin correspond to hESC derived from ICM and Blastomeres respectively.</p

UNS genes grouping showing significant differences between single blastomeres, ICMs and hESCs.

<p>(<b>A</b>) Expression patterns with significant differences are grouped in six clusters according to over-expression or down-regulation after comparative gene expression analysis, giving rise to the totipotency signature (TS) from blastomeres (Clusters 1 and 2), the <i>in vivo</i> pluripotency signature (IVVPS) (Clusters 3 and 4), and the <i>in vitro</i> pluripotency signature (IVTPS). Red box means up-regulated genes, and blue box means down-regulated (Clusters 5 and 6). (<b>B</b>) Genes from the UNS with no significant differences in expression are also included (Cluster 7) and are represented in green. Connector genes are shown in bold. The criteria for statistically significant values was a p-value cutoff of <0.05. Complete data are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062135#pone.0062135.s004" target="_blank">Table S1</a>.</p

Cytoscape analysis of (A) TS, (B) IVVPS, and (C) IVTPS.

<p>Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. Microarray data values represented here are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062135#pone.0062135.s001" target="_blank">Fig S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062135#pone.0062135.s002" target="_blank">S2</a>.</p