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比较两个不同实验差异基因分析的结果并发表文章

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发表于 2017-1-13 11:52:48 | 显示全部楼层 |阅读模式
第一个是在ESCs里面用3种不同shRNAs的敲低Dnmt3L前后都做了芯片数据,发现了777 upregulated and 467 downregulated genes ,差异基因列表见:http://www.sciencedirect.com/sci ... 92867413010878#mmc1

第二个是 2009年发表的EBs里面的 PGC (Stella-positive) versus non-PGC (Stella-negative) 的差异基因列表

它们的上下调基因的韦恩图如下figure C:

(C) A comparison of the genes that are regulated upon Dnmt3L knockdown in ESC against the genes that are differentially expressed in PGCs versus the average of the other differentiating layers.

作者是这样描述这个结果的:
To identify the genes that are regulated by the Dnmt3L, we performed microarray analysis of the three shRNAs (Pearson correlation R ≥ 0.87, Figure S2A).
The microarray analysis of the control and Dnmt3L knockdown ESCs identified 777 upregulated and 467 downregulated genes (Table S1).
To identify among the Dnmt3L-regulated genes those that were involved in ESC differentiation into PGCs, we compared this list of Dnmt3L-regulated genes with the genes that are differentially expressed in PGC (Stella-positive) versus non-PGC (Stella-negative) EBs, which were previously published (West et al., 2009).
This analysis identified 60 genes that are upregulated by Dnmt3L knockdown and that were also upregulated in Stella-negative cells and 67 genes that were downregulated in Dnmt3L knockdown and were also downregulated in Stella-negative cells (Figures 2A and 2B).
Cluster analysis revealed that Dnmt3L was coregulated with three members of the Rhox (reproductive homeobox on X-chromosome) family: Rhox5, Rhox6, and Rhox9 ( Figure 2B).
Further comparison of Dnmt3L-regulated genes versus mouse-derived PGCs and other tissue-regulated genes ( Hayashi et al., 2011, Shen et al., 2008 and Turbendian et al., 2013) confirmed the coregulation of Dnmt3L with Rhox genes ( Figures S2C and S2D).



你能重现这个图吗?





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发表于 2017-1-14 23:40:01 | 显示全部楼层
楼主,能否附上原文题目?我想学习一下!
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发表于 2017-1-15 00:05:24 | 显示全部楼层
没注意有个链接,已经看到了!
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