Differences in gene expression identified using SAPAS analysis.

<p>(A) Scatterplot and MA plot of gene expression using SAPAS in GSCs and ESCs. (B) Hierarchical clustering of differentially expressed genes among samples. (C) GO analysis of GSCs up-regulated (P<0.01, Fisher's exact test and fold change >2) in GSCs. A Bonferroni p-value < 0.001 corrects for errors due to multiple testing. (D) Venn diagram showing overlap between GSC up-regulated genes detected by SAPAS and other studies, including Yang’s [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145417#pone.0145417.ref019" target="_blank">19</a>], others [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145417#pone.0145417.ref020" target="_blank">20</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145417#pone.0145417.ref022" target="_blank">22</a>] and meiosis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145417#pone.0145417.ref027" target="_blank">27</a>]. (E) Venn diagram showing overlap between GSC and ESC up- or down-regulated genes compared to MEFs. GSCs, germline stem cells; MEFs, mouse embryonic fibroblast cells; ESCs, embryonic stem cells.