今天我们讲解JASPAR 数据库(http://jaspar.genereg.net/)的使用!
温馨提示:电脑浏览会更好!
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首先,我们先介绍一下相关的基本概念!
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TFBS的表示形式
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常见的准路因子预测网站
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这里只列出了部分,我们这里这介绍JASPAR
1.JASPAR 简介
Jaspar中有9个子数据库,CORE, CNE, FAM, PBM等,关于什么时候使用哪个数据库,在About下有详细介绍。
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2.主页面介绍
如下是Jaspar主页面,左边是工具栏;中间显示的是数据库中收录的六大类生物,可点击查看每个大类中收集的数据总量;右侧是用户使用导航,第一次使用的用户可以点击JASPAR interactive tour ,可跟随该导航一步步学习网站的使用方法。
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3.检索TF
点击左侧工具栏中search,查找感兴趣的数据。可以通过TF名称或ID、物种、分类单元、uniprot ID或任何其他关键字进行搜索。Advanced Options为高级检索,以检索人的转录因子SP1为例,下方可选框中选择筛选要求,快速锁定目标数据。
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搜索结果被展示在一个列表中。一般我们选择最新版本!
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点击ID号,跳转至SP1 motif详情,包括文件摘要、序列logo图、PFM矩阵(文件可下载)、TF-binding信息(FASTA格式为该motif在基因组范围的结合区域的序列,bed格式为该motif在基因组范围的结合位点,可点击下载)、外部链接、版本信息、ChIP-seq centrality、TFFM和其它信息。
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4.转录因子预测
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