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如何从Science文章中挖掘出新方向

2015-07-17 四月23 GCBI

经常拜读大牛们发表的Science和Nature,但是我们可不可以从这些文章中学到精髓,也来发表一篇高分论文呢? 举个例子,比方说发表在Science上的这篇文章The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation,我们得知:抑制lnc-DC可破坏体外人类外周血单

经常拜读大牛们发表的Science和Nature,但是我们可不可以从这些文章中学到精髓,也来发表一篇高分论文呢?

举个例子,比方说发表在Science上的这篇文章The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation,我们得知:抑制lnc-DC可破坏体外人类外周血单核细胞以及体内的小鼠骨髓细胞分化为DC,并减小了DCs刺激T细胞活化能力。lnc-DC通过激活转录因子STAT3来调节这些效应,lnc-DC直接结合细胞质中的STAT3上,通过阻止STAT3结合SHP1及脱磷酸作用,提高STAT3在tyrosine-705上磷酸化。这篇文章主要涉及的内容有树突状细胞的分化和功能,来搜索一下“Dendritic cell differentiation and function”,搜索结果很多,可以设置“影响因子”和“是否拥有样本”缩小范围来进行下一步筛选。如果只是简单的翻阅文章可能理解的还不够深入,我们可以使用文章提供的样本来还原作者的实验思路,甚至还有可能发现更多。


图1 搜索结果及筛选工具

图2 Science文章及样本界面

OK,就看Science这篇文章,文章和样本中提到Monocytes经过6个时间点分化为Dendritic Cell,而这批数据通过HTA 2.0芯片检测可获得mRNA、lncRNA表达数据。根据从GCBI-Sample下载的数据(GSE54143),首先我们可以分析mRNA、lncRNA随分化时间而发生表达变化的趋势,同时对mRNA进行GO、Pathway分析,不仅如此,我们还可以分析lncRNA调控mRNA的共表达网络,找到核心调控lncRNA和mRNA。


图3 拓展分析思路图

运行方案后稍等10-20分钟,就可以查看各部分详细结果并下载完整的结果报告。结果很多,包括刚才提到的显著mRNA、lncRNA及其趋势等,而在共表达网络图部分发现一些核心基因CCL22、TFRC、SELL、IL23A、FOSB。


图4 lncRNA和mRNA共表达网络图

这些基因不了解没关系,接下来再回到知识库以Immune为关键词检索文献,发现共有905027篇,而与刚才提到的基因相关的文献分别为:CCL22(36篇)、TFRC(20篇)、SELL(106篇)、IL23A(176篇),而FOSB只有3篇。通过Dictionary查询,发现FOSB参与破骨细胞分化信号通路,样本为诱导单核细胞分化为树突状细胞,bingo!然而在microRNA部分只有has-miR-224-5p已经被验证过,由于最近ceRNA研究很热,这可以作为下一个研究课题。

好的,我们来梳理一下:文章提到了转录因子STAT3和lnc-DC之间的关系,通过对数据的挖掘再分析,发现核心基因FOSB以及相关miRNA,而这些都是文章没有提到同时研究很少,那么我们是不是可以做点什么了?

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  1. [GetPortalCommentsPageByObjectIdResponse(id=256478, encodeId=3b9e2564e86d, content=学习了, beContent=null, objectType=article, channel=null, level=null, likeNumber=103, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://wx.qlogo.cn/mmopen/vi_32/Q0j4TwGTfTJNCjP5GJqqBZFlbk1Dm8cXyP7gpY57Ut698B6phuTyicrxr4kcWYkhhCCeAmco6PFOMa0JSribUP9A/0, createdBy=cfcb2174142, createdName=wangvase, createdTime=Fri Oct 27 23:00:00 CST 2017, time=2017-10-27, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=89581, encodeId=07ed8958130, content=好深奥, beContent=null, objectType=article, channel=null, level=null, likeNumber=130, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=b9d01623203, createdName=wuxclove, createdTime=Sun Jun 12 14:58:00 CST 2016, time=2016-06-12, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=41601, encodeId=261a4160125, content=不理解,基础还是不足, beContent=null, objectType=article, channel=null, level=null, likeNumber=123, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=df9e1651052, createdName=三三五五, createdTime=Tue Oct 27 20:35:00 CST 2015, time=2015-10-27, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=33129, encodeId=cd0933129a4, content=好文章, beContent=null, objectType=article, channel=null, level=null, likeNumber=112, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=http://thirdwx.qlogo.cn/mmopen/vi_32/Q0j4TwGTfTIKlpu9buib1TxXRibfFuzYXHaLxQgfUpwzYwTMo8551BS40KVZNRDLWmAXSibjfnFm0QggOrCSWElfw/132, createdBy=95aa1617853, createdName=happy1, createdTime=Sun Jul 19 22:38:00 CST 2015, time=2015-07-19, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=1375071, encodeId=26c113e50711e, content=<a href='/topic/show?id=2949159989d' target=_blank style='color:#2F92EE;'>#SCIE#</a>, beContent=null, objectType=article, channel=null, level=null, likeNumber=73, replyNumber=0, topicName=null, topicId=null, topicList=[TopicDto(id=15998, encryptionId=2949159989d, topicName=SCIE)], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=17a3387, createdName=jichang, createdTime=Sun Jul 19 08:41:00 CST 2015, time=2015-07-19, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=33078, encodeId=85b4330e85b, content=方向在哪, beContent=null, objectType=article, channel=null, level=null, likeNumber=131, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=cab51623450, createdName=sanshengshi, createdTime=Sun Jul 19 00:01:00 CST 2015, time=2015-07-19, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=33015, encodeId=69fe330157d, content=哈, beContent=null, objectType=article, channel=null, level=null, likeNumber=136, replyNumber=0, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=7ee51614674, createdName=240612799, createdTime=Fri Jul 17 22:53:00 CST 2015, time=2015-07-17, status=1, ipAttribution=)]
    2017-10-27 wangvase

    学习了

    0

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    2016-06-12 wuxclove

    好深奥

    0

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    2015-10-27 三三五五

    不理解,基础还是不足

    0

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    2015-07-19 happy1

    好文章

    0

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    2015-07-19 jichang
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    2015-07-19 sanshengshi

    方向在哪

    0

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    2015-07-17 240612799

    0

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