Predict Binding Sites of Transcription Factor && 富集分析
2017-04-22 15:59
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标题
**1.一般的来说,目前发现的2000个转录因子一般是分为基础性和调控性的,基础性有1300;基础的转录因子与RNA聚合酶一起和启动子区域特异性结合,发挥作用,开始转录;而特异性的一般是和增强子一起结合形成增强体,进而发挥复杂的生物学功效。2.在学习中,我发现一般采用参照motif(转录因子模板)的位置权重矩阵对一段序列(一般是启动子区域的sequence)进行predict;
3还有就是对转录因子进行识别,因为毕竟并不是所有sequence匹配上的gene段都是binding sites,还需要更加精确和复杂的生物学构象才可以决定是否成为对应motify的结合区域,一般是对significance评估,设定阈值,筛选,得到靶序列。
ps:一般进行预测转录因子结合位点,可以上www.gene-regulation.com,可以免费预测。**
transcription factor的富集分析
是我最近看的一篇关于colorectal cancer基因芯片分析了解的,纯属个人观点,欢迎讨论~
1.首先和go,pathway富集一样,对筛选出来的显著基因进行累计超几何分布,或是Fisher精确检验等等的富集方法,FDR校正后卡阈值得到significant的转录因子集合位点;
2.对显著gene卡一个值p,具体根据研究和数据大小定,基因中启动子区域有超过p的筛出来;
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