Motif Enrichment Analyses Obtained By Centrimo On Human Enhancers

We applied Centrimo (Bailey and Machanick 2012) from the MEME suite version 4.11.1 with default parameters to DNA sequences of regions ± 500 bp around the mid-points of enhancers from class 1 (lower %GC) and class 2 (higher %GC). Class 1 enhancer regions were used as foreground and class 2 enhancer regions as background and vice-versa. The MEME databases of motifs<br> considered for enrichment were derived from (Jolma et al. 2013) (jolma2013.meme), JASPAR (Mathelier et al. 2015a) (JASPAR_CORE_2016_vertebrates.meme), Cis-BP (Weirauch et al. 2014) (Homo_sapiens.meme), Swiss Regulon (Pachkov et al. 2013) (Swiss_Regulon_human_and_mouse.meme), and HOCOMOCO (Kulakovskiy et al. 2016) (HOCOMOCOv10_HUMAN_mono_meme_format.meme). The same procedure was applied to promoter regions ( ± 500 bp around gene starts) associated with class 1 and class 2 enhancers.我们采用版本4.11.1的MEME套件（MEME Suite）中的Centrimo工具（Bailey与Machanick, 2012），以默认参数，对1类（GC含量较低）和2类（GC含量较高）增强子中点上下游±500bp区域的DNA序列进行分析。以1类增强子区域作为前景集、2类作为背景集，反之亦然。本次富集分析所选用的MEME基序（motif）数据库，分别来源于Jolma等人2013年的研究（jolma2013.meme）、JASPAR数据库（Mathelier等人2015a，JASPAR_CORE_2016_vertebrates.meme）、Cis-BP数据库（Weirauch等人2014，Homo_sapiens.meme）、Swiss Regulon数据库（Pachkov等人2013，Swiss_Regulon_human_and_mouse.meme）以及HOCOMOCO数据库（Kulakovskiy等人2016，HOCOMOCOv10_HUMAN_mono_meme_format.meme）。将上述完整分析流程应用于与1类和2类增强子相关的启动子区域（基因转录起始位点上下游±500bp区间）。