小伙伴们看了《把Cell爆文的思路、方法用到自己的研究中》都想知道：找到关键转录因子的这个图是怎么画的？
Figure S5. Motif Dynamics, Related to Figure 3 (A) Enrichment scores of transcription factor binding motifs for the DHSs in human and mouse embryos.
出自Gao, L., Wu, K., Liu, Z., Yao, X., Yuan, S., & Tao, W., et al. (2018). Chromatin accessibility landscape in human early embryos and its association with evolution.Cell. 详见《把Cell爆文的思路、方法用到自己的研究中》
彩色版
Figure 4 d. TF motif analysis of different regions in the human genome CGI in DMVs, non-CGI in DMVs, CGI in all promoters, and non-CGI in all promoters. The scale of the circles represents motif enrichment. Red represents homeobox TFs.
出自Li, Y., Zheng, H., Wang, Q., Zhou, C., Wei, L., Liu, X., Zhang, W., Zhang, Y., Du, Z., Wang, X. and Xie, W., 2018. Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biology, 19(1), p.18. 详情见《任意两组RNA-seq变身，国自然得AAA》
还有用颜色代表表达量的：
Figure 4 Identification of candidate regulators for early development. a, TF motifs identified from distal ATAC-seq peaks. Only TFs expressed at least at one stage (FPKM ≥ 5) and motif enrichment P value <1 × 10−10 at least at one stage were included.
出自Wu, J., Huang, B., Chen, H., Yin, Q., Liu, Y., Xiang, Y., ... & Li, W. (2016). The landscape of accessible chromatin in mammalian preimplantation embryos. Nature, 534(7609), 652.详见《表观遗传是怎样遗传的？| 颉伟讲怎样用ATAC-seq研究表观遗传机制的视频》
到底怎么画呢？方法来啦！
上面三篇paper用的都是HOMER，又一款motif分析利器！
The script findMotifsGenome.pl in HOMER software was used to analyze transcription factors binding motifs enrichment in DHSs (Heinz et al., 2010).
http://homer.ucsd.edu/homer/ngs/peakMotifs.html
用HOMER的findMotifsGenome.pl算出P-value，然后跟RNA-seq的表达值FPKM一起作为输入，在R里面画图。
熟悉clusterProfiler的小伙伴儿，一定觉得这些图跟下面这个图很像，详见《最靠谱的富集分析，超炫的展示方式，TCGA也是他的粉丝》：
击鼓传花，3，2，1，开始：
怎样用HOMER找motif？@生信技能树
怎样用HOMER算出的P-value画出CNS级别的泡泡图？@Y叔