24小时热门版块排行榜

返回列表

琴心健魄

铁虫 (初入文坛)

应助: 0 (幼儿园)
金币: 189.7
帖子: 42
在线: 28.9小时
虫号: 4035149
注册: 2015-08-24
专业: 遗传学与生物信息学

[求助] 芯片数据分析时，如何利用差异gene list 构建 gene network 图已有1人参与

求助有经验的同学，我现在有用450k甲基化芯片分析的得到的差异甲基化基因位点，
接下来想做一系列后续分析，有几个问题如下：
1）一个cg位点的ucsc基因注释经常有不只一个，而同一个基因有时有能对上好多个cg位点，这个各位都是如何处理的？
2）在得到差异基因列表后，如何构建那种好看的网状图（network analysis），经常看到别人的甲基化组学文章里有这样的图，貌似都是拿IPA画的，可是IPA是异常昂贵的收费软件，而且我也没有理解画出图的含义，有用过IPA的求解释
有没有其他好的方法？STRING貌似可以？
3）network analysis时，是先对甲基化谱做了pathway分析，再选出最显著的pathway，用这个pathway的所有基因构建网络图，不知道我这样的理解对吗？

问题有点多，谢谢你的耐心阅读！如果有的东西太基础不想一个个回答的话，
有相应的教程或是能学到这些知识的资源还请推荐共享一下，谢谢！

IPA revealed that many differentially methylated genes are present in networks known to be involved in OA. The first network identified centered on SMAD3 (itself hypomethylated in our assay), which functions in a highly correlated manner with TGF to maintain articular cartilage (45) (Figure 3A). A second network included the aforementioned NFATC1, HTRA1, and DLX5. Akt was central in this network, which upregulates MMP production through hypoxia-inducible factor 2 and NF-B and contributes to OA pathology (Figure 3B) (46). Both of these networks demonstrate likely indirect effects of differentially methylated genes on known OA effector pathways

芯片数据分析时，如何利用差异gene list 构建 gene network 图-1

Molecular network analysis with Ingenuity software resulted in a very likely network (score 40), that revealed several “hidden hubs” consisting of molecules involved in skeletal homeostasis, such as type I collagen, alkaline phosphatase, and NF-B (Figure 3). The network was enriched in genes associated with the development of the appendicular skeleton (P 0.00006), limb morphogenesis (P < 0.0014), and osteoblast differentiation (P <0.0001).

回复此楼

» 本帖附件资源列表

欢迎监督和反馈：小木虫仅提供交流平台，不对该内容负责。
本内容由用户自主发布，如果其内容涉及到知识产权问题，其责任在于用户本人，如对版权有异议，请联系邮箱：xiaomuchong@tal.com
附件 1 : Genome-Wide_DNA_Methylation_Study_Identifies_S.pdf

2016-08-29 10:48:03, 582.67 K