鸿源韬生物

WGBS生信分析报告

1.项目简介

1.1 样本信息

合同编号 RS2411002
实验技术 WGBS
物种名称 拟南芥
拉丁名 Arabidopsis thaliana
参考基因组 tair10
报告生成日期 2025年07月02日
客户送样名称 测序数据名称 分组
SDG2ZF-1 SDG2ZF_rep1 SDG2ZF
SDG2ZF-2 SDG2ZF_rep2 SDG2ZF
SDG2ZF-3 SDG2ZF_rep3 SDG2ZF
Rdd-1 Rdd_rep1 Rdd
Rdd-2 Rdd_rep2 Rdd
Rdd-3 Rdd_rep3 Rdd


1.2 实验原理及流程

全基因组DNA甲基化测序（WGBS，Whole Genome Bisulfite Sequencing）是一种单碱基分辨率鉴定全基因组范围内DNA 甲基化水平的技术，是研究DNA甲基化的黄金标准。该技术的主要原理是通过对DNA 样本进行亚硫酸盐处理，未甲基化的胞嘧啶（C）被亚硫酸盐转化为尿嘧啶（U），而甲基化的胞嘧啶则不受影响。转化后的DNA 随后进行文库构建和高通量测序，通过比较处理后的DNA 序列与参考基因组序列的差异，可以准确地定位和量化DNA甲基化位点（Zamudio N et al., 2015）。WGBS 技术允许研究者深入理解甲基化在基因表达调控、生长发育以及疾病形成中的作用，是表观遗传学研究的高效工具。WGBS 能为基因组DNA甲基化时空特异性修饰的研究提供重要技术支持，能广泛应用在个体发育、衰老和疾病等生命过程的机制研究中，也是各物种甲基化图谱研究的首选方法。



1.3 实验流程


WGBS实验主要步骤有五步:
(1)样本准备与DNA提取​,从细胞或组织中提取高质量基因组DNA； (2)亚硫酸盐处理基因组DNA,DNA经亚硫酸氢钠（NaHSO₃）处理，在碱性条件下将未甲基化的胞嘧啶（C）脱氨基为尿嘧啶（U），而甲基化的胞嘧啶（5mC）保持不变； (3)PCR扩增与文库构建​​,转化后的DNA进行PCR扩增,添加测序接头，之后纯化与富集DNA； (4)​​高通量测序​​，使用二代测序平台进行双端测序，生成双端短读长（paired-end reads）数据； (5)生物信息分析，鉴定全基因组5mC位点。


WGBS实验原理


进行高通量测序上机前必须要构建与之匹配的测序文库，测序文库的主要构建流程如下：
(1)对IP下来的 DNA进行片段化与接头连接；
(2)将DNA片段进行PCR扩增，富集带有接头的DNA片段；
(3)利用磁珠纯化回收目的大小片段，获得待测序文库；
(4)利用琼脂糖电泳方法对所构建的文库进行质检；
(5)利用Qubit4.0对文库进行定量，确定文库浓度是否适合上机;
(6)文库质检合格后，把不同文库按照有效浓度及目标下机数据量的需求在测序仪上进行上机测序。

DNA文库构建

1.4 分析流程

获得测序原始数据（raw data）后，首先对原始数据进行过滤，获得高质量的测序数据（clean data），将测序数据（clean data）比对到项目物种的碱基转换（C->T,G->A）后参考基因组上，对比对结果进行鉴定甲基化位点，对高甲基化区域（区域内所有CpG位点的平均甲基化水平大于70%）关联基因进行注释以及富集分析，有生物学重复时进行差异甲基化区域（Differential Methylation Regions,DMR）分析。


WGBS生物信息学分析流程



2. 数据质控

我们交付的原始数据为fastq（简称fq）格式文件的压缩包，文件名后缀通常为 “.fq.gz”。交付数据前我们会计算每个压缩文件的md5值。在您拿到数据之后，请您先校>验每个压缩文件的md5值，Linux下可以在数据目录使用“md5sum -c <*md5.txt>”命令进行校验，Windows下可使用hashmyfiles等校验工具，如发现压缩文件md5值与附在数据文件目录下的md5文档中的不一致则说明文件可能在传输的过程中被损坏。数据文件大小为文件占用磁盘空间的大小，文件的大小通常与磁盘格式、压缩比例等因素有关，与测序数据量（碱基数）的多少无对应关系，因此对应PE测序的 read1和read2两个文件大小也可能不相同。

将高通量测序得到的原始图像数据经过Base Calling 转化为序列数据，即FASTQ格式，得到最原始的测序数据文件。FASTQ 格式文件可记录所测读段（read）的碱基及其质量分数。FASTQ 格式以测序读段为单位进行存储，每条读段占 4 行，第一行是序列标识（read ID）以及相关的描述信息，以“@” 开头；第二行即为碱基序列，长度由测序策略决定；第三行以“+”开头，后面是序列标示符、描述信息，或者什么也不加； 第四行是测序质量值（phred），与第二行一一对应，phred值以ASCII码标记，对应的 ASCII 值减去33，即为第二行对应碱基的测序质量值，示例如下：

@HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT
NAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT
+
#55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHH

测序错误率用e表示， 平台测得数据的碱基质量值用Qphred表示，则有：Qphred=-10log10(e)。软件中碱基识别正确率与Phred分值之间的简明对应关系见下表：

Phred分值不正确的碱基识别碱基正确识别率Q-score
101/1090%Q10
201/10099%Q20
301/100099.9%Q30

测序Reads的错误率往往会随着测序接近尾声而升高，这是由测序过程中化学试剂的消耗造成共有的特征。



2.1 原始数据质控

ChIP-Seq实验基于第二代测序（NGS）平台完成，采用双端测序文库构建策略（插入片段~300 bp）。我们需要对原始测序数据进行质量评估与过滤，以确保后续分析的可靠性。首先，我们使用FastQC（version 0.12.1）(Andrews, 2010)对原始测序数据（raw data）进行全局质量分析，包括碱基质量分布（Phred score）、碱基组成平衡性（base content uniformity）、重复序列比例（duplication level）及GC含量偏差等指标，以全面评估测序质量。
我们使用Fastp（version 0.24.0）(Chen et al., 2018)对原始测序数据进行以下过滤操作。
接头序列去除：识别并切除双端reads中的接头序列；
低复杂度序列过滤：剔除含模糊碱基（N碱基占比≥10%）的reads；
动态质量修剪：通过滑动窗口法（5 bp窗口步长）评估局部序列质量，当窗口平均Phred score小于20时，执行3'端截断；
长度筛选：保留长度≥25 bp的paired-end reads，长度不足的reads及其匹配reads（R1/R2）均被排除。
原始和过滤后质控结果请详见result/1.qc文件夹，raw为原始数据质控结果，clean为过滤后质控结果。



图2.1 各个样本平均测序碱基质量分数，横坐标代表150 bp长度序列中各个位置，纵坐标为该位置平均的碱基质量值Q；盒形图中间的红线表示中位数（median value）；黄色部分代表四分位距（25-75%）；上下分割线代表 90%和 10%的上下临界值；蓝色的线代表碱基质量的平均值。


图2.2 各个样本碱基平衡性，图中四条线代表A T C G在每个位置平均含量。理论上，A和T应该相等，G和C应该相等，且4种碱基平行且接近分布。正常情况下四种碱基的出现频率应该是接近的，而且没有位置差异。因此好的样本中四条线应该平行且接近。当部分位置碱基的比例出现 bias 时，即四条线波动较大时可能存在测序数据或者文库污染。如果所有位置的碱基比例一致的表现出bias 时，即四条线平行但分开，往往代表文库有 bias (建库过程或本身特点)，或者是测序中的系统误差。测序刚开始由于测序仪状态不稳定，在15bp之前很可能出现波动。


图2.3 各个样本重复序列水平，测序深度越高，越容易产生一定程度的重复（duplication），这属于正常的现象。但如果duplication 的程度很高，就提示我们可能有 bias 的存在（如建库过程中由于 PCR 扩增引起的duplication）。横坐标为 reads 重复的次数，纵坐标为重复次数对应的 reads 占 unique reads 的比例，以unique reads 的总数作为 100%。这里，我们仅对文件前 2000000 个reads 进行统计：对长度小于75bp 的reads 将其截短为 50bp，用于统计重复。


2.2 过滤后数据质控

这里展示Fastp过滤后的数据质控结果，图片内容与上面raw data类似。

图2.4 各个样本平均测序碱基质量分数，横坐标代表150 bp长度序列中各个位置，纵坐标为该位置平均的碱基质量值Q；盒形图中间的红线表示中位数（median value）；黄色部分代表四分位距（25-75%）；上下分割线代表 90%和 10%的上下临界值；蓝色的线代表碱基质量的平均值。

图2.5 各个样本碱基平衡性，图中四条线代表A T C G在每个位置平均含量。理论上，A和T应该相等，G和C应该相等，且4种碱基平行且接近分布。正常情况下四种碱基的出现频率应该是接近的，而且没有位置差异。因此好的样本中四条线应该平行且接近。当部分位置碱基的比例出现 bias 时，即四条线在某些位置波动较大时，可能测序数据或者文库存在污染。当所有位置的碱基比例一致的表现出bias 时，即四条线平行但分开，往往代表文库有 bias (建库过程或本身特点)，或者是测序中的系统误差。一般测序的时候，刚开始测序仪状态不稳定，在15bp之前很可能出现波动。

图2.6 各个样本重复序列水平，测序深度越高，越容易产生一定程度的重复（duplication），这属于正常的现象。但如果duplication 的程度很高，就提示我们可能有 bias 的存在（如建库过程中由于 PCR 扩增引起的duplication）。横坐标为 reads 重复的次数，纵坐标为重复次数对应的 reads 占 unique reads 的比例，以unique reads 的总数作为 100%。这里，我们仅对文件前 2000000 个reads 进行统计：对长度小于75bp 的reads 将其截短为 50bp，用于统计重复。



2.3 数据过滤结果统计

我们对数据过滤结果进行统计，如下表所示：

Sample Raw_Total_Reads Raw_Total_Bases Raw_Q20_Rate Raw_Q30_Rate Raw_GC_Content Clean_Total_Reads Clean_Total_Bases Clean_Q20_Rate Clean_Q30_Rate Clean_GC_Content
Rdd_rep1 290.36M 29325.95M 0.974 0.926 0.204 286.70M 27989.69M 0.978 0.931 0.191
Rdd_rep2 71.12M 7183.09M 0.976 0.930 0.206 70.10M 6818.59M 0.980 0.936 0.190
Rdd_rep3 228.78M 23106.90M 0.959 0.903 0.237 213.68M 20447.24M 0.976 0.927 0.189
SDG2ZF_rep1 266.96M 26962.88M 0.973 0.924 0.214 263.07M 25498.01M 0.977 0.931 0.197
SDG2ZF_rep2 294.83M 29777.48M 0.973 0.924 0.209 289.32M 28082.71M 0.977 0.930 0.189
SDG2ZF_rep3 245.62M 24807.79M 0.961 0.907 0.244 227.69M 21874.43M 0.977 0.930 0.194

表 2.1数据过滤结果统计：
Sample：样品名称；
Raw_Total_Reads/Clean_Total_Reads：过滤前后样本总reads数量，单位为百万；
Raw_Total_Bases/Clean_Total_Bases：过滤前后样本总碱基数量，单位为百万；
Raw_Q20_Rate/Clean_Q20_Rate：过滤前后样本Q20碱基比例；
Raw_Q30_Rate/Clean_Q30_Rate：过滤前后样本Q30碱基比例；
Raw_GC_Content/Clean_GC_Content:过滤前后样本GC含量。







3. 比对参考基因组

我们将各样品过滤后的clean data的reads与参考基因组进行比对，获取Reads在参考基因组上的定位信息，这里使用的软件是Bismark（version 0.24.2）(Krueger F, Andrews SR, 2011)与Bowtie2(version 2.4.5)(Langmead B. et al., 2018)。首先，Bismark将参考基因组序列进行转换模拟bisulfite处理的基因组序列，生成C->T和G->A两套参考基因组。之后，使用bowtie2，将亚硫酸氢盐测序产生的短读长（reads）比对到处理后参考基因组，生成BAM格式的比对结果（包含reads的位置、质量及比对得分等信息）；随后，bismark解析该BAM文件，针对亚硫酸氢盐处理的特性（未甲基化C→U，甲基化C保持C），识别CpG、CHG、CHH等位点的甲基化状态——通过比对原始reads与转化后的参考序列，统计每个C位点在reads中的保留（甲基化）或转化（未甲基化）比例，最终输出各位点的甲基化水平（如甲基化百分比）及统计结果。

3.1 比对参考基因组情况

sample clean_reads unique_reads unmap mutlimap rmdup_reads rmdup_ratio
Rdd_rep1 143,351,011 113,805,354 15,389,381 14,156,276 90,413,625 63.07%
Rdd_rep2 35,048,829 27,616,641 3,900,271 3,531,917 23,874,750 68.12%
Rdd_rep3 106,838,474 72,849,993 23,926,014 10,062,467 30,786,011 28.82%
SDG2ZF_rep1 131,535,990 101,314,235 14,504,291 15,717,464 82,661,720 62.84%
SDG2ZF_rep2 144,659,262 112,828,564 15,043,332 16,787,366 82,136,029 56.78%
SDG2ZF_rep3 113,846,861 85,716,454 16,433,454 11,696,953 65,443,442 57.48%

表 3.1比对结果统计：
sample：样品名称；
clean_reads：clean后reads总数；
unique_reads：比对到唯一区域reads数量；
unmap：未比对上的reads数量；
mutlimap：比对到多个区域的reads数量；
rmdup_reads：去除PCR重复后唯一比对reads数量；
rmdup_ratio：去除PCR重复后唯一比对reads占总reads（clean_reads）百分比。




3.2 甲基化情况

某位置的甲基化水平可根据未转化为T的C与转化为T的C的reads的比例计算得到，甲基化水平=C-reads数量/(C+T reads数量)。基化的C所处的上下文环境，分成以下3类：1. CpG、2. CHG、3. CHH。p代表磷酸二酯键，CpG指的是甲基化的C的下游是1个G碱基。H代表除了G碱基之外的其他碱基，即A, C, T中的任意一种，CHG代表甲基化的C下游的2个碱基是H和G, CHH表示甲基化的C下游的两个碱基都是H。

sample all_Cytosine CpG_count CpG_ratio CHG_count CHG_ratio CHH_count CHH_ratio
Rdd_rep1 2,115,792,618 75,110,756 26.9% 25,431,173 9.0% 42,287,265 2.7%
Rdd_rep2 552,797,895 18,396,512 25.1% 6,222,888 8.5% 10,659,353 2.6%
Rdd_rep3 655,577,780 23,180,010 27.4% 9,703,285 11.2% 17,685,988 3.6%
SDG2ZF_rep1 1,937,431,797 70,752,436 26.9% 23,175,153 8.6% 34,813,946 2.5%
SDG2ZF_rep2 1,890,766,328 64,080,245 25.3% 20,343,467 8.0% 30,408,472 2.2%
SDG2ZF_rep3 1,482,423,621 52,036,410 27.0% 21,983,451 11.1% 41,568,419 3.8%

表 3.1 各样本甲基化统计：
sample：样品名称；
all_Cytosine：用于分析的胞嘧啶数目；
CpG_count：甲基化的CpG位点数目；
CpG_ratio：甲基化的CpG位点占全部CpG context比例；
CHX_count：甲基化的CHG/GHH位点数目；
CHX_ratio：甲基化的CHG/GHH位点占全部CHG/GHH context比例。




3.3 甲基化水平可视化

全基因组甲基化水平是一个压缩的“.bw”格式文件，它的值代表区域内平均甲基化水平百分比，下限为0，上限100(位于report/result/3.bw文件夹中)。客户可以结合物种参考基因组和注释文件使用IGV (Integrative Genomics Viewer) 浏览器对bam、bw、bed等文件进行可视化浏览。IGV浏览器使用方法可参考我们提供的使用说明文档IGV快速上手




4. 差异甲基化区域分析

在存在多个分组且组内有生物学重复的情况下，可以对组间进行差异甲基化区域（Differential Methylation Regions,DMR）分析，以确定哪些区域甲基化水平在组间存在显著差异。如果没有差异分析则本节内容为空。

4.1 差异甲基化区域分析结果

存在组内生物学重复时，我们使用软件DMRfinder(version 0.3)(Gaspar JM, Hart RP., 2017)有效识别具有差异甲基化CpG位点的基因组区域。结果详见report/result/4.diff。后文中提到的“diff”代表组间差异。
Diff:“group1_result.tsv”为第一个比较组样本差异分析未过滤结果，group1_sig.tsv为根据p值过滤后显著性差异区域（默认p < 0.05且甲基化水平差距大于0.1为显著性差异）。



显示前100行 (共2954行)
chr start end CpG Rdd:mu SDG2ZF:mu Rdd->SDG2ZF:diff Rdd->SDG2ZF:pval
1 6683 6817 6 0.101 0.206 0.106 0.000
1 56674 56742 4 0.273 0.638 0.364 0.000
1 264303 264435 5 0.573 0.675 0.102 0.014
1 368991 369157 5 0.003 0.131 0.129 0.005
1 428249 428303 5 0.328 0.683 0.355 0.000
1 743369 743489 4 0.139 0.387 0.248 0.000
1 816340 816617 12 0.421 0.528 0.107 0.009
1 878936 879129 8 0.490 0.622 0.132 0.005
1 1220748 1220986 4 0.098 0.250 0.153 0.000
1 1344364 1344374 3 0.615 0.922 0.307 0.001
1 1344496 1344553 6 0.771 0.902 0.132 0.003
1 1359177 1359398 11 0.434 0.552 0.118 0.004
1 1371987 1372386 10 0.531 0.422 -0.109 0.007
1 1400006 1400353 9 0.462 0.354 -0.108 0.007
1 1589359 1589505 7 0.657 0.888 0.231 0.031
1 1591861 1591965 4 0.429 0.134 -0.295 0.000
1 1699536 1699874 10 0.483 0.615 0.131 0.001
1 1711206 1711254 5 0.323 0.483 0.160 0.044
1 1717708 1717745 4 0.486 0.598 0.112 0.022
1 1720915 1721075 6 0.119 0.252 0.134 0.000
1 1743274 1743460 5 0.038 0.313 0.276 0.015
1 1867402 1867672 10 0.252 0.356 0.103 0.014
1 2094795 2094932 3 0.453 0.571 0.118 0.006
1 2100507 2100946 12 0.618 0.722 0.105 0.004
1 2157967 2158284 18 0.416 0.558 0.142 0.020
1 2162222 2162363 7 0.206 0.335 0.129 0.004
1 2600737 2600834 3 0.307 0.082 -0.225 0.000
1 2619856 2619926 5 0.549 0.703 0.154 0.000
1 2672976 2673278 9 0.281 0.401 0.121 0.004
1 2691549 2691739 9 0.399 0.544 0.146 0.003
1 2835992 2836030 3 0.318 0.452 0.133 0.008
1 2845863 2846120 13 0.514 0.362 -0.152 0.025
1 2887336 2887655 8 0.441 0.741 0.300 0.001
1 2916751 2916825 4 0.096 0.210 0.115 0.009
1 2953714 2954159 13 0.499 0.602 0.103 0.009
1 2977545 2977681 4 0.126 0.226 0.100 0.009
1 3221490 3221591 5 0.375 0.560 0.185 0.016
1 3364545 3364826 9 0.522 0.630 0.108 0.007
1 3407288 3407336 6 0.197 0.370 0.173 0.011
1 3428405 3428486 3 0.079 0.296 0.218 0.001
1 3510264 3510328 3 0.246 0.400 0.154 0.002
1 3531480 3531542 6 0.234 0.385 0.151 0.019
1 3550704 3550859 9 0.053 0.286 0.234 0.000
1 3551274 3551361 4 0.720 0.871 0.151 0.009
1 3552632 3552777 6 0.367 0.773 0.406 0.000
1 3552920 3553067 9 0.413 0.730 0.317 0.000
1 3555959 3556183 9 0.359 0.472 0.113 0.005
1 3586070 3586147 3 0.665 0.563 -0.102 0.022
1 3608602 3608625 3 0.502 0.620 0.118 0.006
1 3661387 3661477 6 0.571 0.692 0.121 0.005
1 3722151 3722265 3 0.150 0.497 0.347 0.021
1 3769749 3770109 6 0.020 0.168 0.148 0.000
1 3825593 3825719 5 0.689 0.388 -0.302 0.029
1 3855592 3855661 3 0.384 0.528 0.144 0.049
1 3970905 3970988 3 0.256 0.090 -0.166 0.014
1 4002705 4003035 13 0.434 0.550 0.116 0.004
1 4090890 4090974 6 0.184 0.459 0.275 0.001
1 4176431 4176482 4 0.561 0.662 0.101 0.023
1 4237916 4237993 4 0.110 0.243 0.133 0.000
1 4268125 4268215 4 0.114 0.228 0.114 0.011
1 4307211 4307471 7 0.728 0.610 -0.118 0.002
1 4321249 4321534 7 0.437 0.324 -0.113 0.005
1 4412561 4412684 4 0.213 0.380 0.167 0.008
1 4414697 4414951 8 0.118 0.229 0.112 0.001
1 4459664 4460045 11 0.214 0.323 0.109 0.002
1 4507268 4507441 11 0.160 0.057 -0.102 0.045
1 4582567 4582590 3 0.646 0.905 0.259 0.042
1 4604144 4604490 10 0.075 0.239 0.164 0.000
1 4607478 4607635 7 0.105 0.229 0.124 0.002
1 4717228 4717251 4 0.153 0.304 0.151 0.006
1 4787719 4787744 3 0.026 0.287 0.261 0.001
1 4811239 4811306 3 0.002 0.199 0.196 0.001
1 4860861 4860928 3 0.004 0.227 0.223 0.002
1 4896909 4897019 3 0.436 0.722 0.286 0.001
1 4917240 4917265 3 0.086 0.264 0.177 0.000
1 4966315 4966688 8 0.850 0.691 -0.159 0.001
1 5056446 5056714 5 0.759 0.887 0.128 0.007
1 5127814 5128179 10 0.288 0.480 0.192 0.015
1 5331020 5331173 6 0.463 0.638 0.174 0.003
1 5358841 5359170 5 0.835 0.694 -0.141 0.000
1 5359390 5359498 3 0.437 0.805 0.368 0.002
1 5559532 5559622 4 0.008 0.132 0.124 0.005
1 5579471 5579487 3 0.148 0.266 0.118 0.048
1 5582422 5582433 3 0.811 0.935 0.124 0.033
1 5602143 5602276 4 0.469 0.594 0.124 0.040
1 5634810 5634843 3 0.568 0.859 0.291 0.011
1 5717723 5717860 4 0.824 0.933 0.109 0.014
1 5720782 5720896 4 0.458 0.578 0.120 0.010
1 5809081 5809129 5 0.376 0.574 0.199 0.003
1 5830293 5830553 11 0.161 0.289 0.128 0.004
1 5950315 5950390 5 0.581 0.686 0.105 0.025
1 5951586 5951831 9 0.115 0.253 0.138 0.009
1 5955341 5955608 8 0.128 0.236 0.107 0.003
1 5965254 5965445 10 0.698 0.840 0.141 0.013
1 5972387 5972606 4 0.709 0.591 -0.118 0.002
1 5991428 5991502 3 0.450 0.595 0.145 0.017
1 5992009 5992169 4 0.310 0.420 0.110 0.008
1 6007734 6007936 10 0.217 0.346 0.130 0.003
1 6078038 6078059 3 0.746 0.635 -0.111 0.006
1 6163489 6163590 4 0.794 0.906 0.113 0.011

表 4.1 差异甲基化区域分析结果 chr：染色体名称；
start：起始位置；
end：结束位置；
CpG：CpG位点数目；
对照组名称:mu :对照组平均甲基化水平，上限为1；
实验组名称:mu ：实验组平均甲基化水平，上限为1；
对照组->实验组:diff ：实验组与对照组的组间甲基化水平差异；
对照组->实验组:pval ：p值。



图4.1 比较组PCA图。主成分分析是将原来较多维度的指标 (CpG的分布特征)，降维到较低的维度（二维），来研究样品间的主成分关系。二维PCA分析结果中，会展示主成分1(PC1) 和主成分2(PC2)分别作为 X 轴和 Y 轴的散点图，每个点代表 1 个样本。坐标轴上百分比代表主成分的贡献率，贡献率越大，说明该主成分对样本差异的解释能力越强。如果两个样本距离越远，则说明样本CpG区域的差异越大。 反之，则说明相应样本CpG区域整体分布模式越接近。所以，PCA 分析常用于评估样本重复性的好坏。理想情况下，生物学重复的样本应该聚类在一起，而不同组间应该可以区分开。



图4.2 差异甲基化区域火山图。横坐标为甲基化水平差异，纵坐标为-log10(p-value)，蓝色为显著性下调的区域，红色为显著性上调的区域，灰色NS为非显著性差异的区域。







5. 基因组注释

为了进一步探讨甲基化区域结合位点特征，理解染色质开放区域对基因调控的机制， 使用R包ChIPseeker(version 1.36)(Wang et al., 2022)对区域进行注释，我们统计甲基化区域在各基因功能元件分布情况，并将各个甲基化区域与基因关联。各样本甲基化区域指平均甲基化程度高于70%的高甲基化区域，group_sig代表比较组中甲基化水平显著差异的区域。本节结果请详见位于report/result/5.anno文件夹。

5.1 甲基化区域在基因组分布

图5.1 甲基化区域在基因功能元件上分布饼图。
“promoter（<=1kb）”转录起始点(TSS)上游1kb的启动子区域，它与基因的表达调控密切相关；“promoter（1~2kb）”代表TSS上游1~2kb的启动子区域，“promoter（2~3kb）”代表TSS上游2~3kb的启动子区域。
5'非翻译区（5' UTR）和外显子区域（Exon）与mRNA的稳定性或基因表达的调控有关。
3'非翻译区（3' UTR）、内含子（Intron）、远端基因间区（Distal Intergenic）以及TSS下游区（Downstream），这些区域的调控活动可能涉及长距离的基因调控或影响基因的后续处理和表达。



图5.2 各样本甲基化区域在基因功能元件上分布比例堆叠条状图，samples代表单个样本，group代表差异分析比较组。



图5.3 各样本甲基化区域在TSS(转录起始位点)侧翼分布比例堆叠条状图，samples代表单个样本，group代表差异分析比较组，各元件内容含义见图 6.1。



5.2 区域关联基因注释

各个样本区域关联基因注释结果表部分内容如下，完整信息请查看report/result/5.anno/{样本名称}_Anno.csv表格。{组名}_Anno.csv代表差异分析比较组注释结果。

显示前100行 (共653194行)
seqnames start end width strand score num annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS
1 108 116 9 * 93.346 Rdd_rep1_1 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -3515
1 160 162 3 * 86.204 Rdd_rep1_2 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -3469
1 309 311 3 * 81.404 Rdd_rep1_3 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -3320
1 499 501 3 * 81.916 Rdd_rep1_4 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -3130
1 510 512 3 * 87.396 Rdd_rep1_5 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -3119
1 641 651 11 * 92.430 Rdd_rep1_6 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2980
1 789 791 3 * 92.477 Rdd_rep1_7 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2840
1 808 810 3 * 97.297 Rdd_rep1_8 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2821
1 838 840 3 * 90.924 Rdd_rep1_9 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2791
1 903 912 10 * 92.798 Rdd_rep1_10 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2719
1 947 949 3 * 94.220 Rdd_rep1_11 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2682
1 1323 1325 3 * 83.942 Rdd_rep1_12 Distal Intergenic 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 -2306
1 5458 5466 9 * 89.098 Rdd_rep1_13 Promoter (1-2kb) 1 3631 5899 2269 1 AT1G01010 AT1G01010.1 1827
1 6451 6453 3 * 80.357 Rdd_rep1_14 Distal Intergenic 1 6788 8737 1950 2 AT1G01020 AT1G01020.2 2284
1 7019 7023 5 * 92.431 Rdd_rep1_15 Promoter (1-2kb) 1 6788 8737 1950 2 AT1G01020 AT1G01020.2 1714
1 7033 7035 3 * 90.385 Rdd_rep1_16 Promoter (1-2kb) 1 6788 8737 1950 2 AT1G01020 AT1G01020.2 1702
1 17543 17545 3 * 73.067 Rdd_rep1_17 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -3829
1 17571 17573 3 * 70.060 Rdd_rep1_18 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -3857
1 17639 17641 3 * 87.010 Rdd_rep1_19 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -3925
1 17831 17833 3 * 81.360 Rdd_rep1_20 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -4117
1 17958 17960 3 * 80.050 Rdd_rep1_21 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -4244
1 18104 18106 3 * 91.667 Rdd_rep1_22 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -4390
1 18357 18365 9 * 93.223 Rdd_rep1_23 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -4643
1 18374 18380 7 * 95.423 Rdd_rep1_24 Distal Intergenic 1 11649 13714 2066 2 AT1G01030 AT1G01030.2 -4660
1 18435 18449 15 * 90.779 Rdd_rep1_25 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4672
1 18515 18517 3 * 81.742 Rdd_rep1_26 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4604
1 18539 18541 3 * 88.070 Rdd_rep1_27 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4580
1 18700 18702 3 * 92.605 Rdd_rep1_28 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4419
1 18714 18716 3 * 92.974 Rdd_rep1_29 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4405
1 18754 18756 3 * 90.211 Rdd_rep1_30 Distal Intergenic 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -4365
1 21980 21982 3 * 85.079 Rdd_rep1_31 Promoter (1-2kb) 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -1139
1 22001 22003 3 * 90.427 Rdd_rep1_32 Promoter (1-2kb) 1 23121 31227 8107 1 AT1G01040 AT1G01040.1 -1118
1 24187 24197 11 * 95.787 Rdd_rep1_33 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -88
1 24302 24304 3 * 85.709 Rdd_rep1_34 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -203
1 24311 24313 3 * 94.545 Rdd_rep1_35 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -212
1 24330 24332 3 * 94.235 Rdd_rep1_36 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -231
1 24351 24355 5 * 74.103 Rdd_rep1_37 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -252
1 24413 24415 3 * 92.647 Rdd_rep1_38 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -314
1 24455 24457 3 * 90.786 Rdd_rep1_39 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -356
1 24622 24624 3 * 97.414 Rdd_rep1_40 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -523
1 24746 24748 3 * 88.421 Rdd_rep1_41 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -647
1 24834 24839 6 * 91.624 Rdd_rep1_42 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -735
1 24849 24851 3 * 91.667 Rdd_rep1_43 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -750
1 25064 25066 3 * 94.952 Rdd_rep1_44 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -965
1 25075 25085 11 * 92.893 Rdd_rep1_45 Promoter (<=1kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -976
1 25103 25105 3 * 91.712 Rdd_rep1_46 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1004
1 25123 25125 3 * 96.970 Rdd_rep1_47 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1024
1 25167 25172 6 * 91.607 Rdd_rep1_48 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1068
1 25244 25246 3 * 98.295 Rdd_rep1_49 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1145
1 25332 25334 3 * 82.353 Rdd_rep1_50 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1233
1 25346 25355 10 * 97.667 Rdd_rep1_51 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1247
1 25648 25650 3 * 91.667 Rdd_rep1_52 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1549
1 25666 25673 8 * 94.524 Rdd_rep1_53 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1567
1 25708 25710 3 * 92.297 Rdd_rep1_54 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1609
1 25772 25774 3 * 93.548 Rdd_rep1_55 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1673
1 25782 25784 3 * 96.040 Rdd_rep1_56 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1683
1 25830 25832 3 * 93.750 Rdd_rep1_57 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1731
1 25843 25845 3 * 95.437 Rdd_rep1_58 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1744
1 25861 25866 6 * 92.214 Rdd_rep1_59 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1762
1 25946 25948 3 * 86.873 Rdd_rep1_60 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1847
1 25960 25962 3 * 97.273 Rdd_rep1_61 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1861
1 26087 26089 3 * 92.754 Rdd_rep1_62 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -1988
1 26099 26101 3 * 97.222 Rdd_rep1_63 Promoter (1-2kb) 1 23312 24099 788 2 AT1G03993 AT1G03993.1 -2000
1 26350 26352 3 * 96.429 Rdd_rep1_64 Exon (AT1G01040.1/AT1G01040, exon 8 of 20) 1 28500 28706 207 1 AT1G01046 at1g01046 -2148
1 26360 26367 8 * 93.029 Rdd_rep1_65 Exon (AT1G01040.1/AT1G01040, exon 8 of 20) 1 28500 28706 207 1 AT1G01046 at1g01046 -2133
1 26379 26381 3 * 92.974 Rdd_rep1_66 Exon (AT1G01040.1/AT1G01040, exon 8 of 20) 1 28500 28706 207 1 AT1G01046 at1g01046 -2119
1 26402 26410 9 * 89.864 Rdd_rep1_67 Exon (AT1G01040.1/AT1G01040, exon 8 of 20) 1 28500 28706 207 1 AT1G01046 at1g01046 -2090
1 26557 26564 8 * 90.740 Rdd_rep1_68 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1936
1 26600 26602 3 * 93.000 Rdd_rep1_69 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1898
1 26649 26651 3 * 88.910 Rdd_rep1_70 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1849
1 26728 26732 5 * 87.782 Rdd_rep1_71 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1768
1 26786 26788 3 * 97.561 Rdd_rep1_72 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1712
1 26920 26922 3 * 90.909 Rdd_rep1_73 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1578
1 26959 26961 3 * 91.979 Rdd_rep1_74 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1539
1 27148 27150 3 * 94.737 Rdd_rep1_75 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1350
1 27162 27164 3 * 92.677 Rdd_rep1_76 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1336
1 27184 27186 3 * 95.000 Rdd_rep1_77 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1314
1 27484 27486 3 * 93.124 Rdd_rep1_78 Promoter (1-2kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -1014
1 27499 27503 5 * 93.462 Rdd_rep1_79 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -997
1 27624 27626 3 * 95.918 Rdd_rep1_80 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -874
1 27650 27652 3 * 97.115 Rdd_rep1_81 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -848
1 27843 27845 3 * 92.773 Rdd_rep1_82 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -655
1 27989 27991 3 * 91.667 Rdd_rep1_83 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -509
1 28015 28022 8 * 91.022 Rdd_rep1_84 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -478
1 28032 28034 3 * 92.665 Rdd_rep1_85 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -466
1 28299 28301 3 * 91.624 Rdd_rep1_86 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -199
1 28308 28325 18 * 93.637 Rdd_rep1_87 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 -175
1 28763 28765 3 * 84.392 Rdd_rep1_88 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 263
1 28848 28850 3 * 89.216 Rdd_rep1_89 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 348
1 28859 28861 3 * 97.143 Rdd_rep1_90 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 359
1 28923 28925 3 * 95.625 Rdd_rep1_91 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 423
1 28947 28949 3 * 89.943 Rdd_rep1_92 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 447
1 28958 28966 9 * 93.375 Rdd_rep1_93 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 458
1 28978 28980 3 * 94.057 Rdd_rep1_94 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 478
1 29179 29186 8 * 97.241 Rdd_rep1_95 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 679
1 29206 29208 3 * 88.052 Rdd_rep1_96 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 706
1 29255 29257 3 * 87.896 Rdd_rep1_97 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 755
1 29382 29399 18 * 89.545 Rdd_rep1_98 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 882
1 29427 29439 13 * 91.371 Rdd_rep1_99 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 927
1 29463 29472 10 * 95.495 Rdd_rep1_100 Promoter (<=1kb) 1 28500 28706 207 1 AT1G01046 at1g01046 963

表5.1 关联基因注释。第一列到第五列为区域在基因组位置；第六列score为甲基化百分比；第八列annotation为区域的基因组功能元件身份；第九列到第十三列为关联基因的位置信息； 第十四列geneId为基因ID；第十五列transcriptId为转录本ID；第十六列distanceToTSS为区域到TSS距离。



5.3 区域关联CpG岛注释

CpG岛是基因组中富含胞嘧啶和鸟嘌呤的DNA序列。这些区域在基因组中通常呈现为长片段的高C、G含量，与其他区域的碱基序列有很大差异。CpG岛在基因表达调控中扮演着重要角色。它们通常位于基因启动子的附近，通过甲基化等机制调控基因的转录活性。例如，当CpG岛上的C碱基被甲基化时，基因的表达可能会受到抑制。反之，去甲基化则可能激活基因的表达。CpG shores等概念是根据与CpG island的距离进行定义的，CpG Shores 指的是位于CpG island上下游2kb 以内的区域。我们对各个样本高甲基化水平（平均水平大于70%）以及比较组中显著性差异区域进行CpG区域注释。

图5.4 各样本甲基化区域在各CpG区域分布饼图。


显示前100行 (共653559行)
chr start end score cpgtype
1 108 116 93.346 others
1 160 162 86.204 others
1 309 311 81.404 others
1 499 501 81.916 others
1 510 512 87.396 others
1 641 651 92.430 others
1 789 791 92.477 others
1 808 810 97.297 others
1 838 840 90.924 others
1 903 912 92.798 others
1 947 949 94.220 others
1 1323 1325 83.942 others
1 5458 5466 89.098 others
1 6451 6453 80.357 others
1 7019 7023 92.431 others
1 7033 7035 90.385 others
1 17543 17545 73.067 others
1 17571 17573 70.060 others
1 17639 17641 87.010 others
1 17831 17833 81.360 others
1 17958 17960 80.050 others
1 18104 18106 91.667 others
1 18357 18365 93.223 others
1 18374 18380 95.423 others
1 18435 18449 90.779 others
1 18515 18517 81.742 others
1 18539 18541 88.070 others
1 18700 18702 92.605 others
1 18714 18716 92.974 others
1 18754 18756 90.211 others
1 21980 21982 85.079 others
1 22001 22003 90.427 others
1 24187 24197 95.787 others
1 24302 24304 85.709 others
1 24311 24313 94.545 others
1 24330 24332 94.235 others
1 24351 24355 74.103 others
1 24413 24415 92.647 others
1 24455 24457 90.786 others
1 24622 24624 97.414 others
1 24746 24748 88.421 others
1 24834 24839 91.624 others
1 24849 24851 91.667 others
1 25064 25066 94.952 others
1 25075 25085 92.893 others
1 25103 25105 91.712 others
1 25123 25125 96.970 others
1 25167 25172 91.607 others
1 25244 25246 98.295 others
1 25332 25334 82.353 others
1 25346 25355 97.667 others
1 25648 25650 91.667 others
1 25666 25673 94.524 others
1 25708 25710 92.297 others
1 25772 25774 93.548 others
1 25782 25784 96.040 others
1 25830 25832 93.750 others
1 25843 25845 95.437 others
1 25861 25866 92.214 others
1 25946 25948 86.873 others
1 25960 25962 97.273 others
1 26087 26089 92.754 others
1 26099 26101 97.222 others
1 26350 26352 96.429 others
1 26360 26367 93.029 others
1 26379 26381 92.974 others
1 26402 26410 89.864 others
1 26557 26564 90.740 others
1 26600 26602 93.000 others
1 26649 26651 88.910 others
1 26728 26732 87.782 others
1 26786 26788 97.561 others
1 26920 26922 90.909 others
1 26959 26961 91.979 others
1 27148 27150 94.737 others
1 27162 27164 92.677 others
1 27184 27186 95.000 others
1 27484 27486 93.124 others
1 27499 27503 93.462 others
1 27624 27626 95.918 others
1 27650 27652 97.115 others
1 27843 27845 92.773 others
1 27989 27991 91.667 others
1 28015 28022 91.022 others
1 28032 28034 92.665 others
1 28299 28301 91.624 others
1 28308 28325 93.637 others
1 28763 28765 84.392 others
1 28848 28850 89.216 others
1 28859 28861 97.143 others
1 28923 28925 95.625 others
1 28947 28949 89.943 others
1 28958 28966 93.375 others
1 28978 28980 94.057 others
1 29179 29186 97.241 others
1 29206 29208 88.052 others
1 29255 29257 87.896 others
1 29382 29399 89.545 others
1 29427 29439 91.371 others
1 29463 29472 95.495 others

表5.1 关联基因注释。第一列到第三列为位点在基因组位置；第四列score为甲基化百分比；第五列cpgtype是对应的CpG区域，是否属于CpG island或CpG shores。




6. 基因富集分析

我们使用clusterprofiler(version 4.14.6)(Wu T. et al., 2021)进行GO和KEGG通路富集分析。富集分析结果表格未使用阈值过滤，您可以在表格中查看所有可能富集的通路。

6.1 GO富集分析

GO (Gene Ontology, http://www.geneontology.org) 是基因本体论联合会建立的将全世界所有与基因有关的研究结果进行分类汇总的综合数据库。该数据库标准化了不同数据库中关于基因和基因产物的生物学术语，适用于各物种，对基因和蛋白功能进行限定和描述。利用GO 数据库，可以对甲基化区域相关基因进行富集分析，可以找到不同条件下的甲基化区域相关基因按照其参与的BP(Biological Process, 生物过程)、MF(Molecular Function, 分子功能) 及CC(Cellular Component, 细胞组分) 三个方面进行分类注释。GO 注释有助于理解基因背后所代表的生物学意义。GO功能显著性富集分析给出与基因组背景相比，在相关基因中显著富集的GO功能条目，从而给出与甲基化区域相关基因与哪些生物学功能显著相关。该分析首先把所有相关向Gene Ontology数据库的各个term映射，计算每个term的基因数目，然后应用超几何检验，找出与整个基因组背景相比，在与甲基化区域相关基因中显著富集的GO条目。

下面展示甲基化区域的基因富集GO富集分析部分结果，完整结果请见/result/6.gokegg/*_GO_res.csv。GO富集分析完整结果请详见位于report/result/6.gokegg文件夹的*_GO_res.csv表格文件。

显示前100行 (共3337行)
ONTOLOGY ID Description GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue p.adjust qvalue geneID Count
BP GO:0006974 DNA damage response 342/18711 390/25557 0.877 1.198 6.507 0.000 0.000 0.000 AT1G03190/AT1G04020/AT1G05055/AT1G05120/AT1G05180/AT1G05900/AT1G07370/AT1G07500/AT1G07660/AT1G08130/AT1G08390/AT1G08840/AT1G09815/AT1G10520/AT1G10930/AT1G11060/AT1G11100/AT1G11800/AT1G12370/AT1G12400/... 342
BP GO:0009451 RNA modification 331/18711 380/25557 0.871 1.190 6.161 0.000 0.000 0.000 AT1G03110/AT1G03510/AT1G03530/AT1G04840/AT1G05750/AT1G06140/AT1G06150/AT1G06510/AT1G06560/AT1G06710/AT1G08070/AT1G09190/AT1G09220/AT1G09410/AT1G09800/AT1G10330/AT1G10490/AT1G10910/AT1G11290/AT1G11780/... 331
BP GO:0006325 chromatin organization 266/18711 300/25557 0.887 1.211 6.080 0.000 0.000 0.000 AT1G01225/AT1G02580/AT1G02890/AT1G03365/AT1G03770/AT1G04400/AT1G04570/AT1G05830/AT1G06760/AT1G07820/AT1G08060/AT1G08620/AT1G09060/AT1G09320/AT1G09800/AT1G10240/AT1G12270/AT1G14900/AT1G15215/AT1G17210/... 266
BP GO:0006281 DNA repair 305/18711 348/25557 0.876 1.197 6.121 0.000 0.000 0.000 AT1G03190/AT1G04020/AT1G05055/AT1G05120/AT1G05180/AT1G05900/AT1G07370/AT1G07660/AT1G08130/AT1G08390/AT1G08840/AT1G09815/AT1G10520/AT1G10930/AT1G11060/AT1G11100/AT1G11800/AT1G12370/AT1G12400/AT1G14400/... 305
BP GO:0010629 negative regulation of gene expression 287/18711 330/25557 0.870 1.188 5.680 0.000 0.000 0.000 AT1G01040/AT1G02080/AT1G02580/AT1G03360/AT1G03457/AT1G03770/AT1G05460/AT1G05490/AT1G06230/AT1G06710/AT1G07705/AT1G08060/AT1G08370/AT1G08620/AT1G08830/AT1G09060/AT1G09320/AT1G09570/AT1G09700/AT1G09810/... 287
BP GO:0040029 epigenetic regulation of gene expression 147/18711 161/25557 0.913 1.247 5.200 0.000 0.000 0.000 AT1G01225/AT1G02580/AT1G02890/AT1G03770/AT1G04570/AT1G05830/AT1G08060/AT1G08620/AT1G09060/AT1G09320/AT1G09800/AT1G15215/AT1G17210/AT1G17450/AT1G18610/AT1G21610/AT1G21700/AT1G21970/AT1G30970/AT1G48280/... 147
BP GO:0006401 RNA catabolic process 129/18711 140/25557 0.921 1.259 5.072 0.000 0.000 0.000 AT1G01040/AT1G02080/AT1G03360/AT1G03457/AT1G06710/AT1G07705/AT1G08370/AT1G09700/AT1G09810/AT1G14210/AT1G14220/AT1G14710/AT1G15920/AT1G18070/AT1G22760/AT1G25260/AT1G26110/AT1G27820/AT1G27890/AT1G27960/... 129
BP GO:0090407 organophosphate biosynthetic process 290/18711 338/25557 0.858 1.172 5.260 0.000 0.000 0.000 AT1G01220/AT1G01290/AT1G02880/AT1G06520/AT1G08750/AT1G09430/AT1G09830/AT1G10670/AT1G10700/AT1G11880/AT1G12350/AT1G12730/AT1G13560/AT1G15110/AT1G16560/AT1G17410/AT1G21640/AT1G21980/AT1G22620/AT1G22940/... 290
BP GO:0018193 peptidyl-amino acid modification 244/18711 281/25557 0.868 1.186 5.184 0.000 0.000 0.000 AT1G01920/AT1G02580/AT1G03150/AT1G03920/AT1G04020/AT1G04050/AT1G04210/AT1G04440/AT1G04870/AT1G05830/AT1G09060/AT1G09320/AT1G09730/AT1G10570/AT1G12580/AT1G12680/AT1G13350/AT1G16710/AT1G17770/AT1G18335/... 244
BP GO:0043414 macromolecule methylation 193/18711 219/25557 0.881 1.204 5.006 0.000 0.000 0.000 AT1G01920/AT1G02580/AT1G03110/AT1G04050/AT1G04870/AT1G05830/AT1G06560/AT1G09060/AT1G09320/AT1G13870/AT1G15215/AT1G17770/AT1G24610/AT1G27930/AT1G28060/AT1G30550/AT1G35660/AT1G36310/AT1G36370/AT1G45231/... 193
BP GO:1903047 mitotic cell cycle process 193/18711 219/25557 0.881 1.204 5.006 0.000 0.000 0.000 AT1G02730/AT1G03180/AT1G03290/AT1G03780/AT1G06590/AT1G07270/AT1G11060/AT1G15570/AT1G15660/AT1G15940/AT1G16330/AT1G20590/AT1G20610/AT1G20930/AT1G22920/AT1G32180/AT1G33940/AT1G34460/AT1G44110/AT1G44900/... 193
BP GO:0051276 chromosome organization 200/18711 228/25557 0.877 1.198 4.968 0.000 0.000 0.000 AT1G03180/AT1G03290/AT1G03780/AT1G04730/AT1G06590/AT1G08390/AT1G08600/AT1G08620/AT1G10390/AT1G10930/AT1G11060/AT1G14850/AT1G15660/AT1G15940/AT1G16970/AT1G22260/AT1G22275/AT1G27880/AT1G31360/AT1G44900/... 200
BP GO:1901293 nucleoside phosphate biosynthetic process 137/18711 152/25557 0.901 1.231 4.724 0.000 0.000 0.000 AT1G01220/AT1G09430/AT1G09830/AT1G10670/AT1G10700/AT1G12350/AT1G17410/AT1G21640/AT1G24180/AT1G28960/AT1G29870/AT1G29880/AT1G29900/AT1G30120/AT1G30680/AT1G30820/AT1G31220/AT1G34430/AT1G36160/AT1G36180/... 137
BP GO:0009165 nucleotide biosynthetic process 135/18711 150/25557 0.900 1.229 4.656 0.000 0.000 0.000 AT1G01220/AT1G09430/AT1G09830/AT1G10670/AT1G10700/AT1G12350/AT1G17410/AT1G21640/AT1G24180/AT1G28960/AT1G29870/AT1G29880/AT1G29900/AT1G30120/AT1G30680/AT1G30820/AT1G31220/AT1G34430/AT1G36160/AT1G36180/... 135
BP GO:0000278 mitotic cell cycle 245/18711 287/25557 0.854 1.166 4.675 0.000 0.000 0.000 AT1G02730/AT1G03180/AT1G03290/AT1G03780/AT1G06230/AT1G06590/AT1G07270/AT1G09450/AT1G10430/AT1G11060/AT1G15570/AT1G15660/AT1G15940/AT1G16330/AT1G20570/AT1G20590/AT1G20610/AT1G20930/AT1G22920/AT1G32180/... 245
BP GO:0010608 post-transcriptional regulation of gene expression 193/18711 222/25557 0.869 1.187 4.638 0.000 0.000 0.000 AT1G01040/AT1G01410/AT1G02080/AT1G03360/AT1G05460/AT1G05490/AT1G06710/AT1G07705/AT1G08370/AT1G08830/AT1G09570/AT1G09700/AT1G09810/AT1G10840/AT1G13950/AT1G14790/AT1G15920/AT1G17760/AT1G18070/AT1G21580/... 193
BP GO:0032259 methylation 233/18711 272/25557 0.857 1.170 4.661 0.000 0.000 0.000 AT1G01920/AT1G02100/AT1G02580/AT1G03110/AT1G04050/AT1G04870/AT1G05830/AT1G06560/AT1G09060/AT1G09320/AT1G13870/AT1G15125/AT1G15215/AT1G17770/AT1G21100/AT1G21110/AT1G21120/AT1G23360/AT1G24610/AT1G27930/... 233
BP GO:0031047 regulatory ncRNA-mediated gene silencing 108/18711 118/25557 0.915 1.250 4.502 0.000 0.000 0.000 AT1G01040/AT1G05460/AT1G05490/AT1G08830/AT1G09060/AT1G09700/AT1G14790/AT1G15215/AT1G17760/AT1G19100/AT1G21700/AT1G24706/AT1G31280/AT1G31290/AT1G32490/AT1G48410/AT1G53720/AT1G54440/AT1G56310/AT1G57820/... 108
BP GO:0006310 DNA recombination 160/18711 182/25557 0.879 1.201 4.494 0.000 0.000 0.000 AT1G03180/AT1G03190/AT1G04020/AT1G04650/AT1G05180/AT1G06760/AT1G08390/AT1G10930/AT1G12790/AT1G14900/AT1G15910/AT1G15940/AT1G18800/AT1G20720/AT1G20750/AT1G22260/AT1G22275/AT1G27880/AT1G31360/AT1G31760/... 160
BP GO:0006402 mRNA catabolic process 105/18711 115/25557 0.913 1.247 4.391 0.000 0.000 0.000 AT1G01040/AT1G02080/AT1G03360/AT1G03457/AT1G06710/AT1G07705/AT1G08370/AT1G09700/AT1G09810/AT1G14710/AT1G15920/AT1G18070/AT1G22760/AT1G25260/AT1G26110/AT1G27820/AT1G27890/AT1G27960/AT1G28260/AT1G31500/... 105
BP GO:0006302 double-strand break repair 122/18711 136/25557 0.897 1.225 4.355 0.000 0.000 0.000 AT1G04020/AT1G08130/AT1G08390/AT1G10520/AT1G10930/AT1G11800/AT1G15910/AT1G16970/AT1G18800/AT1G19025/AT1G20720/AT1G20750/AT1G27880/AT1G31360/AT1G31760/AT1G34770/AT1G35530/AT1G44900/AT1G48050/AT1G50840/... 122
BP GO:0016441 post-transcriptional gene silencing 63/18711 66/25557 0.955 1.304 4.085 0.000 0.000 0.000 AT1G01040/AT1G03360/AT1G05460/AT1G05490/AT1G08830/AT1G09700/AT1G14790/AT1G17760/AT1G21580/AT1G31280/AT1G31290/AT1G32490/AT1G48410/AT1G63020/AT1G66700/AT1G69440/AT1G70070/AT1G71800/AT1G73840/AT1G75660/... 63
BP GO:0051246 regulation of protein metabolic process 340/18711 411/25557 0.827 1.130 4.390 0.000 0.000 0.000 AT1G01040/AT1G02080/AT1G03360/AT1G03780/AT1G04020/AT1G04050/AT1G04810/AT1G05840/AT1G05880/AT1G05890/AT1G06060/AT1G07705/AT1G07990/AT1G08370/AT1G09060/AT1G09570/AT1G09700/AT1G09810/AT1G10840/AT1G11980/... 340
BP GO:0051656 establishment of organelle localization 79/18711 85/25557 0.929 1.269 4.114 0.000 0.000 0.000 AT1G01510/AT1G04160/AT1G04450/AT1G04600/AT1G08730/AT1G10430/AT1G13160/AT1G13980/AT1G15660/AT1G17580/AT1G24460/AT1G42550/AT1G48760/AT1G50360/AT1G54385/AT1G54560/AT1G56330/AT1G61000/AT1G64500/AT1G66840/... 79
BP GO:0009259 ribonucleotide metabolic process 182/18711 212/25557 0.858 1.173 4.172 0.000 0.001 0.001 AT1G01710/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G12350/AT1G17410/AT1G20260/AT1G24180/AT1G28960/AT1G29900/AT1G30120/AT1G30680/AT1G30820/AT1G31160/AT1G31220/AT1G31910/AT1G32440/AT1G34430/AT1G36160/... 182
BP GO:0009117 nucleotide metabolic process 250/18711 298/25557 0.839 1.146 4.187 0.000 0.001 0.001 AT1G01220/AT1G01710/AT1G04400/AT1G04410/AT1G09420/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12230/AT1G12350/AT1G17410/AT1G20260/AT1G21640/AT1G24180/AT1G28960/AT1G29870/AT1G29880/AT1G29900/... 250
BP GO:0034655 nucleobase-containing compound catabolic process 157/18711 181/25557 0.867 1.185 4.124 0.000 0.001 0.001 AT1G01040/AT1G02080/AT1G03360/AT1G03457/AT1G05620/AT1G06710/AT1G07705/AT1G08370/AT1G09700/AT1G09810/AT1G14210/AT1G14220/AT1G14230/AT1G14250/AT1G14710/AT1G15920/AT1G18070/AT1G22760/AT1G25260/AT1G26110/... 157
BP GO:0010228 vegetative to reproductive phase transition of meristem 391/18711 479/25557 0.816 1.115 4.199 0.000 0.001 0.001 AT1G01040/AT1G01060/AT1G01350/AT1G03160/AT1G03365/AT1G03457/AT1G03750/AT1G04080/AT1G04210/AT1G04400/AT1G04870/AT1G05150/AT1G05380/AT1G05830/AT1G06070/AT1G08680/AT1G09520/AT1G09730/AT1G10390/AT1G10570/... 391
BP GO:0009260 ribonucleotide biosynthetic process 105/18711 117/25557 0.897 1.226 4.047 0.000 0.001 0.001 AT1G09430/AT1G09830/AT1G10670/AT1G12350/AT1G17410/AT1G24180/AT1G28960/AT1G29900/AT1G30120/AT1G30680/AT1G30820/AT1G31220/AT1G34430/AT1G36160/AT1G36180/AT1G36280/AT1G48605/AT1G54130/AT1G54220/AT1G55810/... 105
BP GO:0046390 ribose phosphate biosynthetic process 109/18711 122/25557 0.893 1.220 4.033 0.000 0.001 0.001 AT1G09430/AT1G09830/AT1G10670/AT1G10700/AT1G12350/AT1G17410/AT1G24180/AT1G28960/AT1G29900/AT1G30120/AT1G30680/AT1G30820/AT1G31220/AT1G34430/AT1G36160/AT1G36180/AT1G36280/AT1G48605/AT1G54130/AT1G54220/... 109
BP GO:0006753 nucleoside phosphate metabolic process 259/18711 310/25557 0.835 1.141 4.134 0.000 0.001 0.001 AT1G01220/AT1G01710/AT1G04400/AT1G04410/AT1G09420/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12230/AT1G12350/AT1G14230/AT1G14250/AT1G17410/AT1G20260/AT1G21640/AT1G24180/AT1G28960/AT1G29870/... 259
BP GO:0000819 sister chromatid segregation 84/18711 92/25557 0.913 1.247 3.925 0.000 0.001 0.001 AT1G03290/AT1G03780/AT1G06590/AT1G08390/AT1G11060/AT1G15660/AT1G15940/AT1G49910/AT1G50490/AT1G61000/AT1G61030/AT1G64960/AT1G69400/AT1G72030/AT1G77600/AT1G77720/AT1G78770/AT1G80810/AT2G20000/AT2G20635/... 84
BP GO:0019693 ribose phosphate metabolic process 188/18711 221/25557 0.851 1.162 3.997 0.000 0.001 0.001 AT1G01710/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12350/AT1G17410/AT1G20260/AT1G24180/AT1G28960/AT1G29900/AT1G30110/AT1G30120/AT1G30680/AT1G30820/AT1G31160/AT1G31220/AT1G31910/AT1G32440/... 188
BP GO:0006650 glycerophospholipid metabolic process 132/18711 151/25557 0.874 1.194 3.953 0.000 0.001 0.001 AT1G05470/AT1G05630/AT1G06520/AT1G08750/AT1G11880/AT1G12730/AT1G13560/AT1G15110/AT1G16560/AT1G17340/AT1G21980/AT1G22620/AT1G25290/AT1G31190/AT1G32200/AT1G34120/AT1G34260/AT1G47510/AT1G48140/AT1G48600/... 132
BP GO:0072528 pyrimidine-containing compound biosynthetic process 43/18711 44/25557 0.977 1.335 3.675 0.000 0.001 0.001 AT1G02880/AT1G17410/AT1G22940/AT1G29900/AT1G30820/AT1G55810/AT1G71100/AT2G16370/AT2G21550/AT2G29630/AT2G34890/AT2G44750/AT3G10030/AT3G12670/AT3G16990/AT3G18680/AT3G20330/AT3G24030/AT3G27190/AT3G27440/... 43
BP GO:0035556 intracellular signal transduction 384/18711 472/25557 0.814 1.111 4.032 0.000 0.001 0.001 AT1G01560/AT1G01790/AT1G01960/AT1G02900/AT1G02970/AT1G03800/AT1G03920/AT1G04310/AT1G04370/AT1G04450/AT1G05200/AT1G05470/AT1G06160/AT1G07270/AT1G07880/AT1G08720/AT1G09000/AT1G09450/AT1G10210/AT1G10940/... 384
BP GO:0006338 chromatin remodeling 122/18711 139/25557 0.878 1.199 3.886 0.000 0.001 0.001 AT1G02580/AT1G04400/AT1G06760/AT1G07820/AT1G08060/AT1G08620/AT1G09320/AT1G14900/AT1G15215/AT1G17520/AT1G18800/AT1G21610/AT1G21700/AT1G30810/AT1G48620/AT1G49950/AT1G54260/AT1G54440/AT1G56460/AT1G57820/... 122
BP GO:0006220 pyrimidine nucleotide metabolic process 34/18711 34/25557 1.000 1.366 3.529 0.000 0.001 0.001 AT1G17410/AT1G29900/AT1G30820/AT1G55810/AT2G16370/AT2G21550/AT2G34890/AT3G10030/AT3G12670/AT3G18680/AT3G20330/AT3G27190/AT3G27440/AT3G27740/AT3G46940/AT3G53900/AT3G54470/AT3G60180/AT3G60961/AT4G02120/... 34
BP GO:0006221 pyrimidine nucleotide biosynthetic process 34/18711 34/25557 1.000 1.366 3.529 0.000 0.001 0.001 AT1G17410/AT1G29900/AT1G30820/AT1G55810/AT2G16370/AT2G21550/AT2G34890/AT3G10030/AT3G12670/AT3G18680/AT3G20330/AT3G27190/AT3G27440/AT3G27740/AT3G46940/AT3G53900/AT3G54470/AT3G60180/AT3G60961/AT4G02120/... 34
BP GO:0006644 phospholipid metabolic process 188/18711 222/25557 0.847 1.157 3.876 0.000 0.002 0.001 AT1G05470/AT1G05630/AT1G06520/AT1G08750/AT1G11880/AT1G12730/AT1G13560/AT1G15110/AT1G16560/AT1G17340/AT1G21980/AT1G22620/AT1G25290/AT1G31190/AT1G31910/AT1G32200/AT1G34120/AT1G34260/AT1G47510/AT1G48140/... 188
BP GO:0010564 regulation of cell cycle process 136/18711 157/25557 0.866 1.183 3.806 0.000 0.002 0.002 AT1G02970/AT1G03180/AT1G03780/AT1G04650/AT1G06590/AT1G07270/AT1G07500/AT1G08390/AT1G10690/AT1G11060/AT1G12790/AT1G15570/AT1G19270/AT1G20930/AT1G22920/AT1G25580/AT1G29400/AT1G33240/AT1G35530/AT1G47570/... 136
BP GO:0055086 nucleobase-containing small molecule metabolic process 328/18711 402/25557 0.816 1.114 3.824 0.000 0.002 0.002 AT1G01220/AT1G01710/AT1G03110/AT1G04400/AT1G04410/AT1G05620/AT1G08200/AT1G09420/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12230/AT1G12350/AT1G12780/AT1G14230/AT1G14250/AT1G17160/AT1G17410/... 328
BP GO:0051640 organelle localization 130/18711 150/25557 0.867 1.184 3.732 0.000 0.003 0.002 AT1G01320/AT1G01510/AT1G02010/AT1G04160/AT1G04450/AT1G04600/AT1G08560/AT1G08730/AT1G08820/AT1G10390/AT1G10430/AT1G11250/AT1G12360/AT1G12470/AT1G13160/AT1G13980/AT1G15290/AT1G15660/AT1G17580/AT1G24460/... 130
BP GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing 46/18711 48/25557 0.958 1.309 3.542 0.000 0.003 0.002 AT1G01040/AT1G05460/AT1G05490/AT1G08830/AT1G09700/AT1G31280/AT1G31290/AT1G32490/AT1G48410/AT1G63020/AT1G66700/AT1G69440/AT1G73840/AT2G16390/AT2G27040/AT2G27880/AT2G28190/AT2G32940/AT2G33540/AT2G33730/... 46
BP GO:0006397 mRNA processing 309/18711 378/25557 0.817 1.117 3.774 0.000 0.003 0.002 AT1G01940/AT1G02840/AT1G03910/AT1G04080/AT1G04510/AT1G06220/AT1G06960/AT1G07350/AT1G07740/AT1G08780/AT1G09140/AT1G09230/AT1G09660/AT1G09760/AT1G09770/AT1G10320/AT1G10910/AT1G11900/AT1G12300/AT1G12700/... 309
BP GO:0032784 regulation of DNA-templated transcription elongation 39/18711 40/25557 0.975 1.332 3.471 0.000 0.003 0.002 AT1G03740/AT1G09600/AT1G18670/AT1G27630/AT1G32130/AT1G33770/AT1G35440/AT1G45233/AT1G53050/AT1G54610/AT1G57700/AT1G63210/AT1G65440/AT1G71530/AT1G74330/AT2G22370/AT2G34210/AT2G38560/AT3G01085/AT3G05050/... 39
BP GO:0006399 tRNA metabolic process 153/18711 179/25557 0.855 1.167 3.717 0.000 0.003 0.002 AT1G03110/AT1G03360/AT1G07910/AT1G08540/AT1G09620/AT1G11475/AT1G11870/AT1G13870/AT1G14610/AT1G18130/AT1G20410/AT1G22660/AT1G25350/AT1G27160/AT1G28350/AT1G29870/AT1G29880/AT1G31600/AT1G34150/AT1G36310/... 153
BP GO:0070646 protein modification by small protein removal 91/18711 102/25557 0.892 1.219 3.657 0.000 0.003 0.002 AT1G02090/AT1G04860/AT1G09730/AT1G10570/AT1G17110/AT1G22920/AT1G28120/AT1G32850/AT1G43690/AT1G47740/AT1G48790/AT1G50670/AT1G51710/AT1G52430/AT1G52450/AT1G60220/AT1G65110/AT1G65120/AT1G65130/AT1G65650/... 91
BP GO:0140014 mitotic nuclear division 77/18711 85/25557 0.906 1.237 3.623 0.000 0.003 0.002 AT1G03180/AT1G03290/AT1G03780/AT1G06590/AT1G11060/AT1G15660/AT1G15940/AT1G49910/AT1G61000/AT1G61030/AT1G64960/AT1G69400/AT1G72030/AT1G77600/AT1G77720/AT1G78770/AT1G80810/AT2G20635/AT2G27170/AT2G28620/... 77
BP GO:0000725 recombinational repair 90/18711 101/25557 0.891 1.217 3.614 0.000 0.003 0.003 AT1G04020/AT1G08390/AT1G10930/AT1G15910/AT1G18800/AT1G27880/AT1G31360/AT1G31760/AT1G35530/AT1G44900/AT1G48580/AT1G52530/AT1G52950/AT1G60930/AT1G64750/AT1G65470/AT1G66740/AT1G67500/AT1G71310/AT1G74560/... 90
BP GO:0006913 nucleocytoplasmic transport 103/18711 117/25557 0.880 1.202 3.628 0.000 0.003 0.003 AT1G02690/AT1G05410/AT1G09270/AT1G10390/AT1G12930/AT1G13120/AT1G13160/AT1G14850/AT1G24310/AT1G24706/AT1G26170/AT1G27970/AT1G33410/AT1G43700/AT1G45233/AT1G55540/AT1G59660/AT1G63540/AT1G63810/AT1G64750/... 103
BP GO:0051169 nuclear transport 103/18711 117/25557 0.880 1.202 3.628 0.000 0.003 0.003 AT1G02690/AT1G05410/AT1G09270/AT1G10390/AT1G12930/AT1G13120/AT1G13160/AT1G14850/AT1G24310/AT1G24706/AT1G26170/AT1G27970/AT1G33410/AT1G43700/AT1G45233/AT1G55540/AT1G59660/AT1G63540/AT1G63810/AT1G64750/... 103
BP GO:0018022 peptidyl-lysine methylation 56/18711 60/25557 0.933 1.275 3.523 0.000 0.003 0.003 AT1G01920/AT1G02580/AT1G04050/AT1G05830/AT1G09060/AT1G09320/AT1G17770/AT1G24610/AT1G51450/AT1G51600/AT1G54440/AT1G73100/AT1G77300/AT2G06210/AT2G16390/AT2G17900/AT2G18850/AT2G22370/AT2G22740/AT2G23380/... 56
BP GO:0009648 photoperiodism 240/18711 290/25557 0.828 1.130 3.692 0.000 0.003 0.003 AT1G01060/AT1G03365/AT1G03457/AT1G03750/AT1G04080/AT1G04210/AT1G04400/AT1G05150/AT1G09730/AT1G10390/AT1G11480/AT1G12110/AT1G12910/AT1G14650/AT1G16210/AT1G17210/AT1G17450/AT1G18450/AT1G18560/AT1G18610/... 240
BP GO:0000724 double-strand break repair via homologous recombination 85/18711 95/25557 0.895 1.222 3.585 0.000 0.003 0.003 AT1G04020/AT1G08390/AT1G10930/AT1G15910/AT1G18800/AT1G27880/AT1G31360/AT1G35530/AT1G44900/AT1G52530/AT1G52950/AT1G60930/AT1G64750/AT1G65470/AT1G66740/AT1G67500/AT1G71310/AT1G74560/AT1G79950/AT2G05642/... 85
BP GO:1901987 regulation of cell cycle phase transition 66/18711 72/25557 0.917 1.252 3.541 0.000 0.003 0.003 AT1G02970/AT1G03180/AT1G06590/AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G25580/AT1G47570/AT1G49910/AT1G50490/AT1G52530/AT1G66740/AT1G69400/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/AT1G77720/... 66
BP GO:0000070 mitotic sister chromatid segregation 65/18711 71/25557 0.915 1.250 3.494 0.000 0.004 0.003 AT1G03290/AT1G03780/AT1G06590/AT1G11060/AT1G15660/AT1G15940/AT1G49910/AT1G61000/AT1G61030/AT1G64960/AT1G69400/AT1G72030/AT1G77600/AT1G77720/AT1G78770/AT1G80810/AT2G20635/AT2G27170/AT2G28620/AT2G32590/... 65
BP GO:0009218 pyrimidine ribonucleotide metabolic process 29/18711 29/25557 1.000 1.366 3.259 0.000 0.004 0.004 AT1G17410/AT1G29900/AT1G30820/AT1G55810/AT2G34890/AT3G10030/AT3G12670/AT3G18680/AT3G20330/AT3G27190/AT3G27440/AT3G27740/AT3G53900/AT3G54470/AT3G60180/AT3G60961/AT4G02120/AT4G09320/AT4G11010/AT4G20320/... 29
BP GO:0009220 pyrimidine ribonucleotide biosynthetic process 29/18711 29/25557 1.000 1.366 3.259 0.000 0.004 0.004 AT1G17410/AT1G29900/AT1G30820/AT1G55810/AT2G34890/AT3G10030/AT3G12670/AT3G18680/AT3G20330/AT3G27190/AT3G27440/AT3G27740/AT3G53900/AT3G54470/AT3G60180/AT3G60961/AT4G02120/AT4G09320/AT4G11010/AT4G20320/... 29
BP GO:0046486 glycerolipid metabolic process 160/18711 189/25557 0.847 1.156 3.566 0.000 0.004 0.004 AT1G05470/AT1G05630/AT1G06520/AT1G08750/AT1G11880/AT1G12730/AT1G13560/AT1G15110/AT1G16560/AT1G17340/AT1G21980/AT1G22620/AT1G25290/AT1G30010/AT1G31190/AT1G32200/AT1G33270/AT1G34120/AT1G34260/AT1G47510/... 160
BP GO:0098813 nuclear chromosome segregation 121/18711 140/25557 0.864 1.181 3.541 0.000 0.004 0.004 AT1G03180/AT1G03290/AT1G03780/AT1G06590/AT1G08390/AT1G11060/AT1G12790/AT1G15660/AT1G15940/AT1G22260/AT1G22275/AT1G48360/AT1G49910/AT1G50490/AT1G53490/AT1G61000/AT1G61030/AT1G64960/AT1G66170/AT1G67370/... 121
BP GO:0007059 chromosome segregation 155/18711 183/25557 0.847 1.157 3.521 0.000 0.005 0.004 AT1G03180/AT1G03290/AT1G03780/AT1G06590/AT1G08390/AT1G11060/AT1G12790/AT1G15660/AT1G15940/AT1G20570/AT1G22260/AT1G22275/AT1G48360/AT1G49890/AT1G49910/AT1G50490/AT1G50710/AT1G53490/AT1G61000/AT1G61030/... 155
BP GO:0006479 protein methylation 82/18711 92/25557 0.891 1.217 3.454 0.000 0.005 0.004 AT1G01920/AT1G02580/AT1G04050/AT1G04870/AT1G05830/AT1G09060/AT1G09320/AT1G17770/AT1G24610/AT1G27930/AT1G51450/AT1G51600/AT1G54440/AT1G63490/AT1G73100/AT1G77300/AT1G78190/AT1G79915/AT2G06210/AT2G16390/... 82
BP GO:0008213 protein alkylation 82/18711 92/25557 0.891 1.217 3.454 0.000 0.005 0.004 AT1G01920/AT1G02580/AT1G04050/AT1G04870/AT1G05830/AT1G09060/AT1G09320/AT1G17770/AT1G24610/AT1G27930/AT1G51450/AT1G51600/AT1G54440/AT1G63490/AT1G73100/AT1G77300/AT1G78190/AT1G79915/AT2G06210/AT2G16390/... 82
BP GO:0007062 sister chromatid cohesion 42/18711 44/25557 0.955 1.304 3.334 0.000 0.005 0.004 AT1G04730/AT1G11060/AT1G15940/AT1G61030/AT1G72030/AT1G77600/AT1G79890/AT1G80810/AT2G20635/AT2G27170/AT2G40550/AT2G44580/AT2G47980/AT3G09880/AT3G10440/AT3G13170/AT3G14190/AT3G44960/AT3G54670/AT3G59550/... 42
BP GO:0009894 regulation of catabolic process 162/18711 192/25557 0.844 1.152 3.506 0.000 0.005 0.004 AT1G01040/AT1G02080/AT1G03360/AT1G04810/AT1G05880/AT1G05890/AT1G06710/AT1G07705/AT1G08370/AT1G09700/AT1G09810/AT1G10430/AT1G13460/AT1G15920/AT1G18070/AT1G20200/AT1G20780/AT1G22740/AT1G22760/AT1G27320/... 162
BP GO:0007018 microtubule-based movement 58/18711 63/25557 0.921 1.257 3.383 0.000 0.006 0.005 AT1G01950/AT1G09170/AT1G12430/AT1G18550/AT1G20060/AT1G21730/AT1G55550/AT1G59540/AT1G63640/AT1G72250/AT1G73860/AT2G21300/AT2G21380/AT2G22610/AT2G28620/AT2G36200/AT2G37420/AT3G10180/AT3G10310/AT3G12020/... 58
BP GO:0009150 purine ribonucleotide metabolic process 157/18711 186/25557 0.844 1.153 3.460 0.000 0.006 0.005 AT1G01710/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G12350/AT1G17410/AT1G20260/AT1G24180/AT1G28960/AT1G30120/AT1G31160/AT1G31220/AT1G31910/AT1G32440/AT1G34430/AT1G36160/AT1G36180/AT1G36280/AT1G47840/... 157
BP GO:0007346 regulation of mitotic cell cycle 67/18711 74/25557 0.905 1.237 3.371 0.000 0.006 0.005 AT1G03180/AT1G06230/AT1G06590/AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G47570/AT1G49910/AT1G50490/AT1G52530/AT1G63100/AT1G66740/AT1G67580/AT1G69400/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/... 67
BP GO:0051168 nuclear export 62/18711 68/25557 0.912 1.245 3.349 0.000 0.007 0.006 AT1G10390/AT1G13120/AT1G13160/AT1G14850/AT1G24706/AT1G33410/AT1G45233/AT1G55540/AT1G59660/AT1G63540/AT1G63810/AT1G64750/AT1G66260/AT1G67120/AT1G72320/AT1G72560/AT1G79280/AT1G80680/AT1G80670/AT2G03820/... 62
BP GO:0044770 cell cycle phase transition 97/18711 111/25557 0.874 1.194 3.379 0.000 0.007 0.006 AT1G02970/AT1G03180/AT1G06590/AT1G07270/AT1G15570/AT1G16330/AT1G20590/AT1G20610/AT1G20930/AT1G22920/AT1G25580/AT1G34460/AT1G44110/AT1G47210/AT1G47220/AT1G47230/AT1G47570/AT1G49910/AT1G50490/AT1G52530/... 97
BP GO:0009250 glucan biosynthetic process 125/18711 146/25557 0.856 1.169 3.394 0.000 0.007 0.006 AT1G02730/AT1G03130/AT1G03310/AT1G05570/AT1G05610/AT1G06490/AT1G09790/AT1G10670/AT1G11000/AT1G14080/AT1G14100/AT1G14110/AT1G16860/AT1G18690/AT1G27070/AT1G27680/AT1G28490/AT1G30010/AT1G30230/AT1G32180/... 125
BP GO:0051726 regulation of cell cycle 212/18711 257/25557 0.825 1.127 3.375 0.000 0.009 0.007 AT1G02970/AT1G03180/AT1G03780/AT1G04650/AT1G06230/AT1G06590/AT1G07270/AT1G07370/AT1G07500/AT1G08390/AT1G10690/AT1G11060/AT1G12790/AT1G15570/AT1G16330/AT1G18040/AT1G19270/AT1G20590/AT1G20610/AT1G20930/... 212
BP GO:0072521 purine-containing compound metabolic process 222/18711 270/25557 0.822 1.123 3.361 0.000 0.009 0.008 AT1G01710/AT1G03110/AT1G04410/AT1G05620/AT1G09420/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12230/AT1G12350/AT1G17410/AT1G20260/AT1G21640/AT1G24180/AT1G28960/AT1G30120/AT1G31160/AT1G31220/... 222
BP GO:0046777 protein autophosphorylation 146/18711 173/25557 0.844 1.153 3.332 0.000 0.010 0.008 AT1G01540/AT1G05100/AT1G06390/AT1G08680/AT1G08720/AT1G09000/AT1G09020/AT1G09970/AT1G11350/AT1G11440/AT1G12580/AT1G12680/AT1G12970/AT1G16130/AT1G16670/AT1G20930/AT1G30570/AT1G35670/AT1G49180/AT1G51790/... 146
BP GO:0045814 negative regulation of gene expression, epigenetic 60/18711 66/25557 0.909 1.242 3.250 0.000 0.010 0.008 AT1G02580/AT1G03770/AT1G08060/AT1G08620/AT1G09320/AT1G15215/AT1G21610/AT1G54440/AT1G57820/AT1G60170/AT1G65470/AT1G66050/AT1G69770/AT2G16390/AT2G16485/AT2G23380/AT2G23740/AT2G27040/AT2G28240/AT2G35160/... 60
BP GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process 237/18711 290/25557 0.817 1.116 3.292 0.000 0.012 0.010 AT1G02145/AT1G04810/AT1G05880/AT1G05890/AT1G06590/AT1G08450/AT1G09060/AT1G09080/AT1G09100/AT1G09210/AT1G10230/AT1G12855/AT1G14400/AT1G14570/AT1G15740/AT1G16190/AT1G16900/AT1G17280/AT1G19750/AT1G20140/... 237
BP GO:0044839 cell cycle G2/M phase transition 32/18711 33/25557 0.970 1.324 3.084 0.000 0.012 0.010 AT1G02970/AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G52530/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/AT2G29680/AT2G31580/AT2G38620/AT2G40430/AT2G44950/AT3G02680/AT3G02860/AT3G18730/AT3G48750/... 32
BP GO:0006163 purine nucleotide metabolic process 205/18711 249/25557 0.823 1.125 3.264 0.000 0.013 0.011 AT1G01710/AT1G04410/AT1G09420/AT1G09430/AT1G09780/AT1G09830/AT1G10670/AT1G10700/AT1G12230/AT1G12350/AT1G17410/AT1G20260/AT1G21640/AT1G24180/AT1G28960/AT1G30120/AT1G31160/AT1G31220/AT1G31910/AT1G32440/... 205
BP GO:0048285 organelle fission 201/18711 244/25557 0.824 1.125 3.248 0.000 0.013 0.011 AT1G03180/AT1G03290/AT1G03780/AT1G04030/AT1G04650/AT1G05180/AT1G06590/AT1G09020/AT1G11060/AT1G12790/AT1G14830/AT1G15660/AT1G15940/AT1G20720/AT1G20750/AT1G20830/AT1G22260/AT1G22275/AT1G25580/AT1G29400/... 201
BP GO:0045786 negative regulation of cell cycle 58/18711 64/25557 0.906 1.238 3.149 0.001 0.014 0.012 AT1G02970/AT1G04650/AT1G06590/AT1G07270/AT1G25580/AT1G33240/AT1G35530/AT1G47570/AT1G49620/AT1G49910/AT1G52530/AT1G62050/AT1G66740/AT1G69400/AT1G71760/AT1G77320/AT1G77620/AT1G77720/AT1G80710/AT2G18290/... 58
BP GO:0140053 mitochondrial gene expression 58/18711 64/25557 0.906 1.238 3.149 0.001 0.014 0.012 AT1G11870/AT1G12300/AT1G12700/AT1G19290/AT1G29880/AT1G30010/AT1G45332/AT1G47278/AT1G48520/AT1G52160/AT1G52620/AT1G62750/AT1G62910/AT1G66345/AT1G68990/AT1G74350/AT2G02150/AT2G07715/AT2G17580/AT2G24120/... 58
BP GO:0010498 proteasomal protein catabolic process 252/18711 310/25557 0.813 1.110 3.231 0.001 0.014 0.012 AT1G02145/AT1G04810/AT1G05880/AT1G05890/AT1G06590/AT1G08450/AT1G09060/AT1G09080/AT1G09100/AT1G09210/AT1G10230/AT1G12855/AT1G14400/AT1G14570/AT1G15740/AT1G16190/AT1G16900/AT1G17280/AT1G19310/AT1G19750/... 252
BP GO:0006354 DNA-templated transcription elongation 48/18711 52/25557 0.923 1.261 3.112 0.001 0.014 0.012 AT1G03740/AT1G09600/AT1G18670/AT1G27630/AT1G32130/AT1G33770/AT1G35440/AT1G45233/AT1G53050/AT1G54610/AT1G57700/AT1G63210/AT1G65440/AT1G71530/AT1G74330/AT1G79730/AT2G06210/AT2G19560/AT2G22370/AT2G34210/... 48
BP GO:0018105 peptidyl-serine phosphorylation 88/18711 101/25557 0.871 1.190 3.164 0.001 0.015 0.012 AT1G03920/AT1G04210/AT1G04440/AT1G12580/AT1G12680/AT1G13350/AT1G30640/AT1G35670/AT1G45160/AT1G48490/AT1G49180/AT1G61950/AT1G72710/AT1G73450/AT1G73460/AT1G74740/AT1G76040/AT1G77720/AT2G17290/AT2G17530/... 88
BP GO:0018209 peptidyl-serine modification 88/18711 101/25557 0.871 1.190 3.164 0.001 0.015 0.012 AT1G03920/AT1G04210/AT1G04440/AT1G12580/AT1G12680/AT1G13350/AT1G30640/AT1G35670/AT1G45160/AT1G48490/AT1G49180/AT1G61950/AT1G72710/AT1G73450/AT1G73460/AT1G74740/AT1G76040/AT1G77720/AT2G17290/AT2G17530/... 88
BP GO:0006164 purine nucleotide biosynthetic process 96/18711 111/25557 0.865 1.181 3.165 0.001 0.015 0.012 AT1G09430/AT1G09830/AT1G10670/AT1G10700/AT1G12350/AT1G17410/AT1G21640/AT1G24180/AT1G28960/AT1G30120/AT1G31220/AT1G34430/AT1G36160/AT1G36180/AT1G36280/AT1G48605/AT1G54130/AT1G54220/AT1G55090/AT1G59900/... 96
BP GO:0032786 positive regulation of DNA-templated transcription, elongation 31/18711 32/25557 0.969 1.323 3.024 0.001 0.015 0.012 AT1G03740/AT1G09600/AT1G18670/AT1G27630/AT1G33770/AT1G35440/AT1G45233/AT1G53050/AT1G54610/AT1G57700/AT1G63210/AT1G65440/AT1G71530/AT1G74330/AT3G01085/AT3G05050/AT3G22590/AT4G10010/AT4G12610/AT4G19560/... 31
BP GO:0000956 nuclear-transcribed mRNA catabolic process 62/18711 69/25557 0.899 1.227 3.126 0.001 0.015 0.012 AT1G02080/AT1G03360/AT1G07705/AT1G08370/AT1G15920/AT1G18070/AT1G22760/AT1G25260/AT1G26110/AT1G27820/AT1G27890/AT1G28260/AT1G31500/AT1G33980/AT1G54440/AT1G54490/AT1G60080/AT1G71770/AT1G75660/AT1G76630/... 62
BP GO:0010948 negative regulation of cell cycle process 52/18711 57/25557 0.912 1.246 3.075 0.001 0.016 0.014 AT1G02970/AT1G04650/AT1G06590/AT1G07270/AT1G25580/AT1G33240/AT1G35530/AT1G47570/AT1G49910/AT1G52530/AT1G66740/AT1G69400/AT1G71760/AT1G77320/AT1G77620/AT1G77720/AT1G80710/AT2G18290/AT2G20635/AT2G29680/... 52
BP GO:0070647 protein modification by small protein conjugation or removal 103/18711 120/25557 0.858 1.172 3.129 0.001 0.016 0.014 AT1G02090/AT1G04860/AT1G09730/AT1G10570/AT1G14400/AT1G17110/AT1G22920/AT1G28120/AT1G32850/AT1G43690/AT1G47740/AT1G48790/AT1G50670/AT1G51710/AT1G52430/AT1G52450/AT1G55250/AT1G60220/AT1G65110/AT1G65120/... 103
BP GO:1903311 regulation of mRNA metabolic process 91/18711 105/25557 0.867 1.184 3.119 0.001 0.016 0.014 AT1G01040/AT1G02080/AT1G03360/AT1G06710/AT1G07350/AT1G07705/AT1G08370/AT1G09660/AT1G09700/AT1G09810/AT1G13190/AT1G15920/AT1G16610/AT1G18070/AT1G22760/AT1G27820/AT1G27890/AT1G27960/AT1G30460/AT1G31500/... 91
BP GO:1901990 regulation of mitotic cell cycle phase transition 47/18711 51/25557 0.922 1.259 3.058 0.001 0.016 0.014 AT1G03180/AT1G06590/AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G49910/AT1G50490/AT1G52530/AT1G66740/AT1G69400/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/AT1G77720/AT1G78770/AT2G20635/AT2G29680/... 47
BP GO:0060966 regulation of gene silencing by regulatory ncRNA 23/18711 23/25557 1.000 1.366 2.902 0.001 0.018 0.015 AT1G05490/AT1G09060/AT1G19100/AT1G21700/AT1G54440/AT2G16390/AT2G16485/AT2G33540/AT2G33730/AT2G45620/AT2G46020/AT3G10480/AT3G10490/AT3G24340/AT3G27670/AT3G42670/AT4G03430/AT4G24970/AT5G13130/AT5G19820/... 23
BP GO:1902749 regulation of cell cycle G2/M phase transition 30/18711 31/25557 0.968 1.322 2.964 0.001 0.018 0.015 AT1G02970/AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G52530/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/AT2G29680/AT2G38620/AT2G40430/AT2G44950/AT3G02680/AT3G02860/AT3G48750/AT3G54180/AT4G12620/... 30
BP GO:0000280 nuclear division 169/18711 204/25557 0.828 1.132 3.118 0.001 0.018 0.015 AT1G03180/AT1G03290/AT1G03780/AT1G04030/AT1G04650/AT1G05180/AT1G06590/AT1G11060/AT1G12790/AT1G15660/AT1G15940/AT1G20720/AT1G20750/AT1G22260/AT1G22275/AT1G25580/AT1G29400/AT1G35530/AT1G48360/AT1G49910/... 169
BP GO:0031329 regulation of cellular catabolic process 140/18711 167/25557 0.838 1.145 3.109 0.001 0.018 0.015 AT1G01040/AT1G02080/AT1G03360/AT1G05880/AT1G05890/AT1G06710/AT1G07705/AT1G08370/AT1G09700/AT1G09810/AT1G10430/AT1G13460/AT1G15920/AT1G18070/AT1G20780/AT1G22740/AT1G22760/AT1G27320/AT1G27820/AT1G27890/... 140
BP GO:0044772 mitotic cell cycle phase transition 77/18711 88/25557 0.875 1.195 3.032 0.001 0.021 0.018 AT1G03180/AT1G06590/AT1G07270/AT1G15570/AT1G16330/AT1G20590/AT1G20610/AT1G20930/AT1G22920/AT1G34460/AT1G44110/AT1G47210/AT1G47220/AT1G47230/AT1G49910/AT1G50490/AT1G52530/AT1G66740/AT1G69400/AT1G71230/... 77
BP GO:0000086 G2/M transition of mitotic cell cycle 29/18711 30/25557 0.967 1.320 2.902 0.001 0.023 0.019 AT1G07270/AT1G15570/AT1G20930/AT1G22920/AT1G52530/AT1G71230/AT1G71760/AT1G76540/AT1G77320/AT1G77620/AT2G29680/AT2G31580/AT2G38620/AT2G40430/AT2G44950/AT3G02680/AT3G02860/AT3G18730/AT3G48750/AT3G54180/... 29
BP GO:0006886 intracellular protein transport 389/18711 491/25557 0.792 1.082 3.038 0.001 0.025 0.020 AT1G02010/AT1G02280/AT1G02690/AT1G03000/AT1G04830/AT1G05520/AT1G06210/AT1G06950/AT1G08190/AT1G08560/AT1G09270/AT1G10390/AT1G10730/AT1G11250/AT1G12360/AT1G12470/AT1G12930/AT1G13900/AT1G14850/AT1G15130/... 389

表7.1 GO富集分析部分结果：
ONTOLOGY:GO方面，细胞成分，生物过程或分子功能之一;
ID:GO标识符，GO ID;
Description:GO术语的文字描述;
GeneRatio:该条目基因比例，分子是富集到这个GO条目上的基因的数目，分母是所有甲基化区域关联基因的数目;
BgRatio:背景比例，分母是物种全部有GO注释的基因的数目，分子是这些基因中注释到这个GO条目上面的基因的数目;
RichFactor​​:富集因子（Enrichment Factor）= GeneRatio / BgRatio;
​​FoldEnrichment​:富集倍数（Fold Enrichment）= (富集通路基因数 / 输入基因数) / (背景通路基因数 / 背景总基因数);
​​zScore​:标准化富集得分（基于超几何分布的 Z 值）;
pvalue:富集的p值;
p.adjust:使用BH校正之后的p值;
qvalue:q值,使用FDR校正之后的p值，q-value相比于p-value更加严格,表示p-value产生假阳性的概率;
geneID:富集到这个GO条目上面的具体的基因ID;
Count:富集到这个GO条目上面的基因的数目。




图7.2 甲基化区域关联基因GO气泡图。纵坐标是GO Term 名称，横坐标是对应GO Term 中检出的基因占背景基因的个数，颜色代表显著性，气泡大小代表该条目基因比例。



图7.3 甲基化区域关联基因GO条状图。按照BP、MF、CC三个方面分别展示GO富集结果。纵坐标是GO Term 名称，横坐标值越大显著性越高，如果为0代表qvalue等于1。



6.2 KEGG富集分析

KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) 是日本京都大学构建的基因组信息数据库，它将基因组序列信息与功能信息相结合，提供了一个全面的基因组功能信息资源。在PATHWAY数据库里，包括图解的细胞生化过程如代谢、膜转运、信号传递、细胞周期，还包括同系保守的子通路等信息。KEGG富集分析可以对甲基化区域关联基因进行KEGG通路富集分析。

下面展示区域关联的基因富集KEGG富集分析部分结果，完整结果请见/result/6.gokegg。KEGG富集分析完整结果请详见位于report/result/6.gokegg文件夹的*_KEGG_res.csv表格文件。

显示前100行 (共99行)
ID Description GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue p.adjust qvalue geneID Count
00970 Aminoacyl-tRNA biosynthesis 46/2577 48/3449 0.958 1.283 3.389 0.000 0.010 0.009 AT1G09620/AT1G11870/AT1G14610/AT1G25350/AT1G29870/AT1G29880/AT1G48520/AT1G50200/AT1G66520/AT1G66530/AT1G70980/AT1G72550/AT2G04842/AT2G25840/AT2G31170/AT2G33840/AT3G02660/AT3G02760/AT3G04600/AT3G07420/... 46
00380 Tryptophan metabolism 37/2577 38/3449 0.974 1.303 3.230 0.000 0.010 0.009 AT1G04610/AT1G20620/AT1G20630/AT1G23800/AT1G24100/AT1G44170/AT1G54100/AT1G74100/AT2G20610/AT2G22330/AT2G25840/AT2G30770/AT2G44460/AT2G44470/AT2G44490/AT3G04600/AT3G24360/AT3G44300/AT3G44310/AT3G44320/... 37
03015 mRNA surveillance pathway 73/2577 82/3449 0.890 1.191 3.016 0.001 0.032 0.029 AT1G03960/AT1G10430/AT1G11400/AT1G12920/AT1G13320/AT1G13460/AT1G15200/AT1G16610/AT1G17720/AT1G17760/AT1G17980/AT1G18070/AT1G25490/AT1G27595/AT1G33980/AT1G49760/AT1G51510/AT1G51690/AT1G54450/AT1G58470/... 73
00620 Pyruvate metabolism 66/2577 75/3449 0.880 1.178 2.676 0.003 0.085 0.078 AT1G04410/AT1G08110/AT1G11840/AT1G18500/AT1G23800/AT1G24180/AT1G30120/AT1G32440/AT1G34430/AT1G36160/AT1G44170/AT1G48030/AT1G53240/AT1G53310/AT1G54100/AT1G54220/AT1G59900/AT1G67280/AT1G68750/AT1G74040/... 66
00310 Lysine degradation 15/2577 15/3449 1.000 1.338 2.258 0.012 0.214 0.196 AT1G23800/AT1G44170/AT1G54100/AT3G24360/AT3G48000/AT3G55410/AT4G13360/AT4G16210/AT4G26910/AT4G34240/AT4G36250/AT5G47720/AT5G48230/AT5G55070/AT5G65750 15
00280 Valine, leucine and isoleucine degradation 41/2577 46/3449 0.891 1.193 2.264 0.013 0.214 0.196 AT1G03090/AT1G04710/AT1G06550/AT1G10060/AT1G23800/AT1G44170/AT1G48030/AT1G50090/AT1G50110/AT1G54100/AT1G55510/AT2G14170/AT2G26800/AT2G30650/AT2G30660/AT2G33150/AT3G06810/AT3G06850/AT3G13450/AT3G16950/... 41
04122 Sulfur relay system 14/2577 14/3449 1.000 1.338 2.181 0.017 0.224 0.205 AT1G01290/AT1G16460/AT1G51310/AT1G76170/AT1G79230/AT2G31955/AT2G43760/AT2G44270/AT2G45695/AT3G61113/AT4G10100/AT4G35910/AT5G55130/AT5G65720 14
00020 Citrate cycle (TCA cycle) 52/2577 60/3449 0.867 1.160 2.148 0.018 0.224 0.205 AT1G04410/AT1G09430/AT1G10670/AT1G24180/AT1G30120/AT1G32480/AT1G34430/AT1G48030/AT1G53240/AT1G54220/AT1G54340/AT1G59900/AT1G60810/AT1G65930/AT2G05710/AT2G17130/AT2G18450/AT2G20420/AT2G22780/AT2G34590/... 52
03013 Nucleocytoplasmic transport 100/2577 121/3449 0.826 1.106 2.042 0.023 0.235 0.215 AT1G04170/AT1G07920/AT1G10390/AT1G10840/AT1G11400/AT1G14850/AT1G15200/AT1G16610/AT1G21160/AT1G24706/AT1G28090/AT1G29550/AT1G29590/AT1G33410/AT1G33980/AT1G36730/AT1G45231/AT1G45233/AT1G49760/AT1G51510/... 100
03050 Proteasome 50/2577 58/3449 0.862 1.154 2.030 0.025 0.235 0.215 AT1G04810/AT1G09100/AT1G13060/AT1G16470/AT1G20200/AT1G29150/AT1G45000/AT1G47250/AT1G53750/AT1G53780/AT1G53850/AT1G56450/AT1G64750/AT1G67250/AT1G75990/AT1G77440/AT1G79210/AT2G05840/AT2G20580/AT2G27020/... 50
00250 Alanine, aspartate and glutamate metabolism 41/2577 47/3449 0.872 1.168 1.988 0.028 0.235 0.215 AT1G17290/AT1G23310/AT1G29900/AT1G36280/AT1G48470/AT1G51720/AT1G62800/AT1G65960/AT1G70580/AT1G72330/AT1G79440/AT2G02000/AT2G13360/AT2G16570/AT2G30970/AT2G38400/AT3G17760/AT3G17820/AT3G20330/AT3G24090/... 41
00260 Glycine, serine and threonine metabolism 41/2577 47/3449 0.872 1.168 1.988 0.028 0.235 0.215 AT1G08630/AT1G11860/AT1G14810/AT1G18640/AT1G22020/AT1G31230/AT1G36370/AT1G48030/AT1G54100/AT1G74920/AT2G13360/AT2G17265/AT2G17630/AT2G26080/AT2G38400/AT2G42490/AT3G02020/AT3G10050/AT3G16950/AT3G17240/... 41
03420 Nucleotide excision repair 50/2577 59/3449 0.847 1.134 1.787 0.046 0.348 0.318 AT1G03190/AT1G03810/AT1G05055/AT1G07370/AT1G08130/AT1G09815/AT1G12400/AT1G16190/AT1G18040/AT1G18340/AT1G19750/AT1G21690/AT1G27840/AT1G50840/AT1G55750/AT1G63160/AT1G66750/AT1G73690/AT1G77470/AT1G78650/... 50
00710 Carbon fixation by Calvin cycle 64/2577 77/3449 0.831 1.112 1.715 0.052 0.371 0.339 AT1G04410/AT1G17290/AT1G23310/AT1G32060/AT1G32440/AT1G42970/AT1G43670/AT1G53240/AT1G53310/AT1G62800/AT1G63290/AT1G68750/AT1G70580/AT1G71100/AT1G72330/AT1G79550/AT1G79750/AT2G01140/AT2G01290/AT2G13560/... 64
00650 Butanoate metabolism 20/2577 22/3449 0.909 1.217 1.753 0.057 0.374 0.342 AT1G24180/AT1G30120/AT1G59900/AT1G65960/AT1G79440/AT2G02000/AT2G26800/AT2G31810/AT2G34590/AT3G15290/AT3G17760/AT3G24360/AT3G48560/AT4G11820/AT4G13360/AT4G16210/AT5G17330/AT5G47720/AT5G48230/AT5G50850 20
03018 RNA degradation 47/2577 56/3449 0.839 1.123 1.599 0.070 0.382 0.350 AT1G02080/AT1G03360/AT1G03905/AT1G07705/AT1G21190/AT1G49760/AT1G54490/AT1G55870/AT1G59760/AT1G60080/AT1G65700/AT1G75660/AT1G76630/AT1G76860/AT1G79090/AT2G03870/AT2G17510/AT2G25355/AT2G29560/AT2G33210/... 47
00240 Pyrimidine metabolism 79/2577 97/3449 0.814 1.090 1.546 0.073 0.382 0.350 AT1G06790/AT1G09815/AT1G11475/AT1G14230/AT1G14250/AT1G17410/AT1G29900/AT1G29940/AT1G30820/AT1G50840/AT1G55810/AT1G67320/AT1G67630/AT1G72880/AT1G78650/AT2G02970/AT2G04630/AT2G15430/AT2G16370/AT2G17420/... 79
00071 Fatty acid degradation 35/2577 41/3449 0.854 1.143 1.578 0.076 0.382 0.350 AT1G04710/AT1G06290/AT1G06310/AT1G23800/AT1G32780/AT1G44170/AT1G49430/AT1G54100/AT1G64710/AT1G77120/AT1G77590/AT2G04350/AT2G33150/AT2G35690/AT3G05970/AT3G06810/AT3G23790/AT3G24360/AT3G48000/AT3G51840/... 35
00640 Propanoate metabolism 27/2577 31/3449 0.871 1.166 1.593 0.077 0.382 0.350 AT1G06550/AT1G23800/AT1G36160/AT1G44170/AT1G54100/AT2G14170/AT2G20420/AT2G30650/AT2G30660/AT2G38040/AT3G06810/AT3G24360/AT3G48000/AT4G04320/AT4G13360/AT4G13660/AT4G16210/AT4G17260/AT4G31810/AT4G34240/... 27
00010 Glycolysis / Gluconeogenesis 85/2577 105/3449 0.810 1.083 1.493 0.081 0.382 0.350 AT1G09780/AT1G16300/AT1G23190/AT1G23800/AT1G24180/AT1G30120/AT1G32440/AT1G32780/AT1G34430/AT1G43670/AT1G44170/AT1G47840/AT1G48030/AT1G50460/AT1G54100/AT1G54220/AT1G59900/AT1G64710/AT1G70730/AT1G77120/... 85
04120 Ubiquitin mediated proteolysis 85/2577 105/3449 0.810 1.083 1.493 0.081 0.382 0.350 AT1G04510/AT1G06590/AT1G10230/AT1G14400/AT1G16890/AT1G17280/AT1G19750/AT1G20140/AT1G26830/AT1G27840/AT1G36340/AT1G45050/AT1G50490/AT1G63800/AT1G65040/AT1G70320/AT1G75440/AT1G78770/AT2G02760/AT2G03160/... 85
03008 Ribosome biogenesis in eukaryotes 62/2577 76/3449 0.816 1.092 1.392 0.101 0.455 0.416 AT1G06720/AT1G08410/AT1G10490/AT1G15440/AT1G27470/AT1G43860/AT1G50920/AT1G52980/AT1G54490/AT1G56110/AT1G63780/AT1G63810/AT1G67120/AT1G72710/AT1G75660/AT2G03820/AT2G19470/AT2G21440/AT2G23070/AT2G23080/... 62
00300 Lysine biosynthesis 17/2577 19/3449 0.895 1.197 1.484 0.106 0.455 0.416 AT1G14810/AT1G31230/AT1G54100/AT2G13810/AT2G19940/AT2G44040/AT2G45440/AT3G02020/AT3G14390/AT3G53580/AT3G59890/AT3G60880/AT4G19710/AT5G11880/AT5G13280/AT5G14060/AT5G52100 17
00400 Phenylalanine, tyrosine and tryptophan biosynthesis 36/2577 43/3449 0.837 1.121 1.367 0.114 0.463 0.424 AT1G07780/AT1G22410/AT1G24807/AT1G24909/AT1G25155/AT1G29410/AT1G48850/AT1G48860/AT1G62800/AT1G69370/AT1G71920/AT2G04400/AT2G21940/AT2G29690/AT2G30970/AT2G45300/AT3G06350/AT3G29200/AT3G54640/AT3G55870/... 36
04146 Peroxisome 50/2577 61/3449 0.820 1.097 1.314 0.120 0.463 0.424 AT1G03000/AT1G04710/AT1G06290/AT1G06310/AT1G08830/AT1G20620/AT1G20630/AT1G49430/AT1G54340/AT1G65930/AT1G77590/AT2G04350/AT2G13360/AT2G14860/AT2G26350/AT2G26800/AT2G28190/AT2G33150/AT2G35690/AT2G45690/... 50
00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 12/2577 13/3449 0.923 1.235 1.462 0.122 0.463 0.424 AT1G11880/AT1G63110/AT1G74340/AT2G22530/AT2G34980/AT3G07140/AT3G45100/AT4G35530/AT5G14850/AT5G19130/AT5G22130/AT5G46850 12
00520 Amino sugar and nucleotide sugar metabolism 79/2577 99/3449 0.798 1.068 1.180 0.143 0.525 0.480 AT1G01220/AT1G02730/AT1G05590/AT1G05610/AT1G06780/AT1G08200/AT1G12780/AT1G17890/AT1G18580/AT1G23190/AT1G27680/AT1G30620/AT1G31070/AT1G47840/AT1G50460/AT1G53500/AT1G63000/AT1G63180/AT1G64440/AT1G65590/... 79
04144 Endocytosis 54/2577 67/3449 0.806 1.079 1.118 0.165 0.582 0.532 AT1G10900/AT1G15130/AT1G21980/AT1G47830/AT1G48790/AT1G55180/AT1G56410/AT1G60860/AT1G60890/AT2G06530/AT2G14120/AT2G19830/AT2G26420/AT2G27600/AT2G41210/AT2G42010/AT3G05630/AT3G07960/AT3G08530/AT3G09920/... 54
03022 Basal transcription factors 29/2577 35/3449 0.829 1.109 1.113 0.181 0.597 0.546 AT1G02680/AT1G03280/AT1G04950/AT1G05055/AT1G07470/AT1G18340/AT1G20000/AT1G32750/AT1G54140/AT1G55300/AT1G55750/AT1G73960/AT1G75510/AT3G10070/AT3G10330/AT3G13445/AT3G19040/AT3G29380/AT3G61420/AT4G10680/... 29
00760 Nicotinate and nicotinamide metabolism 10/2577 11/3449 0.909 1.217 1.237 0.191 0.597 0.546 AT1G55090/AT1G72880/AT2G01350/AT2G23420/AT3G21070/AT4G14930/AT4G36940/AT5G14760/AT5G20070/AT5G50210 10
00410 beta-Alanine metabolism 25/2577 30/3449 0.833 1.115 1.090 0.192 0.597 0.546 AT1G06550/AT1G23800/AT1G44170/AT1G54100/AT1G65960/AT1G70310/AT2G02000/AT2G30650/AT2G30660/AT2G42490/AT3G06810/AT3G17760/AT3G17810/AT3G24360/AT3G48000/AT4G04320/AT4G13360/AT4G16210/AT4G31810/AT4G34240/... 25
00052 Galactose metabolism 32/2577 39/3449 0.821 1.098 1.060 0.193 0.597 0.546 AT1G12780/AT1G23190/AT1G47840/AT1G50460/AT1G62660/AT1G63180/AT1G64440/AT1G70730/AT1G72990/AT2G19860/AT2G22480/AT2G36190/AT3G03250/AT3G06580/AT3G10700/AT3G20040/AT3G45940/AT3G54440/AT3G56310/AT4G01970/... 32
00130 Ubiquinone and other terpenoid-quinone biosynthesis 20/2577 24/3449 0.833 1.115 0.974 0.236 0.708 0.647 AT1G06570/AT1G18870/AT1G23360/AT1G60550/AT1G60600/AT1G62940/AT1G65060/AT2G18950/AT2G30920/AT3G11945/AT3G11950/AT3G21240/AT3G24200/AT3G63410/AT4G05160/AT4G23660/AT4G32770/AT5G36160/AT5G53970/AT5G57300 20
03030 DNA replication 36/2577 45/3449 0.800 1.071 0.821 0.264 0.769 0.703 AT1G03810/AT1G07370/AT1G08130/AT1G08840/AT1G09815/AT1G21690/AT1G44900/AT1G50840/AT1G63160/AT1G67320/AT1G67630/AT1G77470/AT1G78650/AT2G06510/AT2G07690/AT2G16440/AT2G25100/AT2G27120/AT2G29570/AT2G33845/... 36
00290 Valine, leucine and isoleucine biosynthesis 29/2577 36/3449 0.806 1.078 0.810 0.275 0.770 0.704 AT1G09620/AT1G10060/AT1G14610/AT1G18500/AT1G24180/AT1G30120/AT1G31180/AT1G50090/AT1G50110/AT1G59900/AT1G74040/AT2G31810/AT2G34590/AT3G10050/AT3G19710/AT3G23940/AT3G48560/AT3G49680/AT3G58610/AT4G04350/... 29
00510 N-Glycan biosynthesis 32/2577 40/3449 0.800 1.071 0.773 0.284 0.770 0.704 AT1G02145/AT1G12990/AT1G16570/AT1G16900/AT1G24320/AT1G30000/AT1G34130/AT1G48140/AT1G67490/AT1G67880/AT1G74340/AT1G76400/AT1G78800/AT2G05320/AT2G13290/AT2G39630/AT2G40190/AT2G41490/AT2G47760/AT3G21160/... 32
00670 One carbon pool by folate 15/2577 18/3449 0.833 1.115 0.843 0.296 0.770 0.704 AT1G11860/AT1G22020/AT1G31220/AT1G36370/AT1G66520/AT2G16370/AT2G35040/AT2G44160/AT4G13890/AT4G17360/AT4G32520/AT4G34570/AT4G37930/AT5G26780/AT5G47435 15
00966 Glucosinolate biosynthesis 15/2577 18/3449 0.833 1.115 0.843 0.296 0.770 0.704 AT1G10060/AT1G18590/AT1G24100/AT1G74090/AT1G74100/AT2G20610/AT2G22330/AT3G19710/AT3G49680/AT4G13770/AT4G31500/AT4G39950/AT5G05260/AT5G23020/AT5G65780 15
00196 Photosynthesis - antenna proteins 18/2577 22/3449 0.818 1.095 0.769 0.312 0.772 0.706 AT1G29910/AT1G29920/AT1G29930/AT1G45474/AT1G61520/AT2G05070/AT2G05100/AT2G34420/AT2G34430/AT2G40100/AT3G08940/AT3G27690/AT3G47470/AT3G54890/AT3G61470/AT4G10340/AT5G28450/AT5G54270 18
00960 Tropane, piperidine and pyridine alkaloid biosynthesis 18/2577 22/3449 0.818 1.095 0.769 0.312 0.772 0.706 AT1G07450/AT1G62800/AT1G71920/AT2G29150/AT2G29260/AT2G29300/AT2G29310/AT2G29320/AT2G29340/AT2G29360/AT2G30670/AT2G42490/AT4G31990/AT5G06060/AT5G11520/AT5G19550/AT5G36160/AT5G53970 18
00330 Arginine and proline metabolism 53/2577 68/3449 0.779 1.043 0.618 0.323 0.780 0.714 AT1G20270/AT1G23800/AT1G44170/AT1G44180/AT1G44820/AT1G48470/AT1G51720/AT1G54100/AT1G62800/AT1G67550/AT1G70310/AT1G75330/AT1G80600/AT2G14260/AT2G16500/AT2G17720/AT2G19940/AT2G22910/AT2G23096/AT2G30970/... 53
00630 Glyoxylate and dicarboxylate metabolism 27/2577 34/3449 0.794 1.063 0.633 0.342 0.789 0.721 AT1G04410/AT1G53240/AT2G05710/AT2G22780/AT2G42790/AT2G44350/AT3G14150/AT3G14420/AT3G15020/AT3G21720/AT3G47520/AT3G58740/AT3G58750/AT3G60100/AT4G17360/AT4G18360/AT4G26970/AT4G35830/AT4G37550/AT4G37560/... 27
04650 Natural killer cell mediated cytotoxicity 14/2577 17/3449 0.824 1.102 0.726 0.343 0.789 0.721 AT1G01560/AT1G07880/AT1G10210/AT1G59580/AT1G64480/AT2G46070/AT3G18430/AT3G59790/AT4G01370/AT4G11330/AT4G26070/AT4G29810/AT4G36450/AT5G55990 14
04141 Protein processing in endoplasmic reticulum 101/2577 132/3449 0.765 1.024 0.485 0.356 0.801 0.733 AT1G04980/AT1G07400/AT1G09210/AT1G10230/AT1G16190/AT1G17280/AT1G20140/AT1G21750/AT1G24320/AT1G27520/AT1G29310/AT1G30000/AT1G34130/AT1G36340/AT1G50670/AT1G53540/AT1G56330/AT1G56410/AT1G65040/AT1G67490/... 101
00100 Steroid biosynthesis 23/2577 29/3449 0.793 1.061 0.571 0.373 0.802 0.734 AT1G07420/AT1G11680/AT1G20050/AT1G50430/AT1G58440/AT2G07050/AT2G22830/AT2G28850/AT2G28860/AT2G29390/AT3G02590/AT3G19820/AT3G45130/AT3G52940/AT4G12110/AT4G34640/AT4G34650/AT4G37760/AT5G13710/AT5G24140/... 23
04712 Circadian rhythm - plant 23/2577 29/3449 0.793 1.061 0.571 0.373 0.802 0.734 AT1G01060/AT1G04400/AT1G09530/AT1G09570/AT1G22770/AT1G68050/AT2G18790/AT2G23070/AT2G23080/AT2G25930/AT2G44680/AT2G46830/AT3G04910/AT3G50000/AT4G08920/AT4G16250/AT4G17640/AT4G18130/AT5G02810/AT5G24470/... 23
04140 Autophagy - animal 10/2577 12/3449 0.833 1.115 0.688 0.382 0.804 0.735 AT1G60490/AT2G05630/AT2G37840/AT2G44140/AT3G53930/AT4G16520/AT4G29380/AT5G17290/AT5G45900/AT5G61500 10
00511 Other glycan degradation 9/2577 11/3449 0.818 1.095 0.543 0.446 0.888 0.812 AT1G05590/AT1G65590/AT1G72990/AT3G26720/AT3G54440/AT3G55260/AT5G05460/AT5G61540/AT5G66150 9
00592 alpha-Linolenic acid metabolism 21/2577 27/3449 0.778 1.041 0.367 0.457 0.888 0.812 AT1G06290/AT1G06310/AT1G13280/AT1G55020/AT1G67560/AT1G72520/AT1G76690/AT2G06050/AT2G35690/AT3G06860/AT3G22400/AT3G25760/AT3G25770/AT3G25780/AT3G45140/AT3G51840/AT4G15440/AT4G16760/AT4G29010/AT5G42650/... 21
00561 Glycerolipid metabolism 27/2577 35/3449 0.771 1.032 0.332 0.458 0.888 0.812 AT1G06520/AT1G23800/AT1G32200/AT1G44170/AT1G51260/AT1G54100/AT1G75020/AT1G80460/AT2G11810/AT2G19450/AT3G11670/AT3G18850/AT3G48000/AT3G56310/AT3G57650/AT4G00400/AT4G00550/AT4G01950/AT4G30580/AT4G31780/... 27
00910 Nitrogen metabolism 33/2577 43/3449 0.767 1.027 0.308 0.459 0.888 0.812 AT1G08065/AT1G11860/AT1G23730/AT1G37130/AT1G48470/AT1G51720/AT1G77760/AT2G15620/AT2G41220/AT3G01500/AT3G10340/AT3G17820/AT3G23490/AT3G44300/AT3G44310/AT3G44320/AT3G47340/AT3G52720/AT3G57050/AT4G20990/... 33
00500 Starch and sucrose metabolism 86/2577 114/3449 0.754 1.010 0.180 0.479 0.888 0.812 AT1G02730/AT1G04920/AT1G05610/AT1G06410/AT1G06780/AT1G11590/AT1G17000/AT1G18580/AT1G23190/AT1G26560/AT1G27680/AT1G47840/AT1G50460/AT1G60140/AT1G61820/AT1G62660/AT1G66430/AT1G68020/AT1G70730/AT1G73370/... 86
00564 Glycerophospholipid metabolism 41/2577 54/3449 0.759 1.016 0.206 0.491 0.888 0.812 AT1G06520/AT1G13560/AT1G15110/AT1G32200/AT1G51260/AT1G55180/AT1G62430/AT1G68000/AT1G74210/AT1G75020/AT1G78690/AT2G32260/AT2G38670/AT2G39290/AT2G42010/AT2G45670/AT3G03530/AT3G03540/AT3G05630/AT3G10370/... 41
00053 Ascorbate and aldarate metabolism 26/2577 34/3449 0.765 1.023 0.236 0.498 0.888 0.812 AT1G14520/AT1G23800/AT1G44170/AT1G54100/AT1G55570/AT1G77490/AT2G19800/AT3G09940/AT3G27820/AT3G29360/AT3G47930/AT3G48000/AT3G52880/AT4G08390/AT4G09010/AT4G32320/AT4G33670/AT4G34240/AT4G35000/AT4G35970/... 26
00350 Tyrosine metabolism 20/2577 26/3449 0.769 1.030 0.260 0.502 0.888 0.812 AT1G06570/AT1G12050/AT1G32780/AT1G62800/AT1G64710/AT1G71920/AT1G77120/AT1G79440/AT2G20340/AT2G30970/AT2G42490/AT3G21300/AT3G27180/AT4G31990/AT5G11520/AT5G19550/AT5G24760/AT5G36160/AT5G43940/AT5G53970 20
00770 Pantothenate and CoA biosynthesis 17/2577 22/3449 0.773 1.034 0.277 0.504 0.888 0.812 AT1G10060/AT1G48605/AT1G50090/AT1G50110/AT2G27490/AT2G31810/AT3G17810/AT3G18030/AT3G19710/AT3G23940/AT3G48560/AT3G49680/AT3G58610/AT4G32180/AT5G12200/AT5G64370/AT5G65780 17
00600 Sphingolipid metabolism 11/2577 14/3449 0.786 1.052 0.332 0.511 0.888 0.812 AT1G27980/AT1G72990/AT3G48780/AT3G48790/AT3G54440/AT3G56310/AT4G04930/AT4G22330/AT4G36480/AT5G08370/AT5G23670 11
00030 Pentose phosphate pathway 40/2577 53/3449 0.755 1.010 0.127 0.523 0.888 0.812 AT1G09420/AT1G12230/AT1G17160/AT1G23190/AT1G43670/AT1G63290/AT1G70730/AT1G71100/AT2G01140/AT2G01290/AT2G22480/AT2G35390/AT2G44530/AT2G45290/AT3G02360/AT3G27300/AT3G49360/AT3G52930/AT3G60750/AT4G24620/... 40
00270 Cysteine and methionine metabolism 63/2577 84/3449 0.750 1.004 0.060 0.535 0.888 0.812 AT1G02500/AT1G14810/AT1G16460/AT1G31230/AT1G33320/AT1G55880/AT1G62380/AT1G62800/AT1G64660/AT1G69770/AT1G70310/AT1G77330/AT1G79230/AT2G05830/AT2G17640/AT2G22810/AT2G30970/AT2G36880/AT2G43750/AT3G02020/... 63
03430 Mismatch repair 25/2577 33/3449 0.758 1.014 0.138 0.538 0.888 0.812 AT1G03810/AT1G07370/AT1G08130/AT1G09815/AT1G21690/AT1G29630/AT1G63160/AT1G65070/AT1G77470/AT1G78650/AT2G06510/AT2G29570/AT2G33845/AT3G18524/AT4G02070/AT4G02460/AT4G09140/AT4G19130/AT4G25540/AT4G28440/... 25
04070 Phosphatidylinositol signaling system 36/2577 48/3449 0.750 1.004 0.045 0.559 0.899 0.822 AT1G10900/AT1G21980/AT1G31190/AT1G49340/AT1G60490/AT1G60890/AT1G62430/AT1G66410/AT1G68000/AT2G26420/AT2G40116/AT2G41210/AT3G07960/AT3G09920/AT3G14270/AT3G19420/AT3G43810/AT3G50110/AT3G55940/AT3G56960/... 36
00230 Purine metabolism 99/2577 133/3449 0.744 0.996 -0.076 0.576 0.899 0.822 AT1G06790/AT1G09815/AT1G09830/AT1G11475/AT1G14230/AT1G14250/AT1G17410/AT1G19920/AT1G23190/AT1G29940/AT1G31220/AT1G32440/AT1G36280/AT1G50840/AT1G63660/AT1G67320/AT1G67550/AT1G67630/AT1G70730/AT1G71750/... 99
01040 Biosynthesis of unsaturated fatty acids 24/2577 32/3449 0.750 1.004 0.037 0.579 0.899 0.822 AT1G01710/AT1G04710/AT1G06290/AT1G06310/AT1G43800/AT2G29980/AT2G33150/AT2G35690/AT2G43710/AT3G02610/AT3G02620/AT3G02630/AT3G03980/AT3G12120/AT3G51840/AT3G55360/AT4G00520/AT4G13180/AT4G16760/AT4G30950/... 24
03410 Base excision repair 29/2577 39/3449 0.744 0.995 -0.052 0.604 0.899 0.822 AT1G05900/AT1G07370/AT1G08130/AT1G09815/AT1G10520/AT1G19480/AT1G50840/AT1G52500/AT1G75090/AT1G75230/AT1G78650/AT1G80420/AT2G27120/AT2G29570/AT2G31320/AT2G31450/AT2G41460/AT3G07930/AT3G12040/AT3G18630/... 29
00480 Glutathione metabolism 46/2577 62/3449 0.742 0.993 -0.096 0.605 0.899 0.822 AT1G02950/AT1G09420/AT1G54340/AT1G63460/AT1G63770/AT1G65820/AT1G65930/AT1G69820/AT1G70310/AT1G77490/AT2G21790/AT2G24200/AT2G25080/AT2G29440/AT2G29460/AT2G29480/AT2G31570/AT2G48150/AT3G02360/AT3G24170/... 46
00051 Fructose and mannose metabolism 37/2577 50/3449 0.740 0.990 -0.118 0.620 0.899 0.822 AT1G01220/AT1G07110/AT1G12000/AT1G17890/AT1G20950/AT1G43670/AT1G47840/AT1G50460/AT1G66430/AT2G01140/AT2G19860/AT2G21170/AT2G22480/AT2G31390/AT2G39770/AT3G02570/AT3G20040/AT3G51160/AT3G52930/AT3G55440/... 37
00061 Fatty acid biosynthesis 20/2577 27/3449 0.741 0.991 -0.077 0.630 0.899 0.822 AT1G08510/AT1G36160/AT1G43800/AT1G62640/AT1G74960/AT2G04540/AT2G05990/AT2G22230/AT2G30200/AT2G38040/AT2G43710/AT3G02610/AT3G02620/AT3G02630/AT3G03980/AT3G25110/AT4G13050/AT4G13180/AT5G10160/AT5G35360 20
00430 Taurine and hypotaurine metabolism 9/2577 12/3449 0.750 1.004 0.023 0.640 0.899 0.822 AT1G65960/AT1G69820/AT2G02000/AT2G42670/AT3G17760/AT3G58670/AT4G29210/AT4G39640/AT5G17330 9
00590 Arachidonic acid metabolism 9/2577 12/3449 0.750 1.004 0.023 0.640 0.899 0.822 AT1G63460/AT1G69820/AT2G25080/AT2G31570/AT2G48150/AT3G63080/AT4G11600/AT4G29210/AT4G39640 9
03440 Homologous recombination 25/2577 34/3449 0.735 0.984 -0.160 0.650 0.899 0.822 AT1G03810/AT1G09815/AT1G10930/AT1G50840/AT1G64750/AT1G78650/AT2G01440/AT2G06510/AT2G19490/AT2G28560/AT2G31970/AT2G32000/AT2G33845/AT3G19210/AT3G20540/AT4G19130/AT4G28440/AT4G30870/AT5G01630/AT5G20850/... 25
00340 Histidine metabolism 14/2577 19/3449 0.737 0.986 -0.104 0.657 0.899 0.822 AT1G23800/AT1G43710/AT1G44170/AT1G54100/AT1G58080/AT1G71920/AT3G21300/AT3G27180/AT3G48000/AT4G14910/AT4G26900/AT4G34240/AT4G36250/AT5G63890 14
00790 Folate biosynthesis 11/2577 15/3449 0.733 0.981 -0.124 0.677 0.899 0.822 AT1G69190/AT1G78660/AT1G78670/AT2G16370/AT2G28880/AT3G11750/AT3G55630/AT4G30000/AT4G34570/AT5G41480/AT5G42370 11
00900 Terpenoid backbone biosynthesis 35/2577 48/3449 0.729 0.976 -0.289 0.683 0.899 0.822 AT1G11755/AT1G17050/AT1G31910/AT1G49530/AT1G78510/AT2G02500/AT2G17370/AT2G17570/AT2G18620/AT2G18640/AT2G23400/AT2G23800/AT2G26930/AT2G34630/AT2G38700/AT3G14510/AT3G14530/AT3G14550/AT3G20160/AT3G21500/... 35
04130 SNARE interactions in vesicular transport 35/2577 48/3449 0.729 0.976 -0.289 0.683 0.899 0.822 AT1G08560/AT1G11250/AT1G13890/AT1G15880/AT1G26670/AT1G29060/AT1G32270/AT1G51740/AT1G79590/AT2G18260/AT2G36900/AT2G45200/AT3G03800/AT3G05710/AT3G09740/AT3G11820/AT3G24315/AT3G24350/AT3G29100/AT3G45280/... 35
00860 Porphyrin metabolism 29/2577 40/3449 0.725 0.970 -0.324 0.702 0.899 0.822 AT1G03475/AT1G08520/AT1G09940/AT1G19670/AT1G44318/AT1G44446/AT1G58290/AT1G69740/AT2G44520/AT3G44880/AT3G48730/AT3G51820/AT3G56090/AT3G56940/AT4G01690/AT4G13250/AT4G18480/AT4G25080/AT4G27440/AT5G04900/... 29
03040 Spliceosome 84/2577 115/3449 0.730 0.978 -0.420 0.706 0.899 0.822 AT1G02840/AT1G04510/AT1G06220/AT1G07360/AT1G09140/AT1G09760/AT1G09770/AT1G14650/AT1G20920/AT1G20960/AT1G21190/AT1G24706/AT1G28060/AT1G32490/AT1G44910/AT1G51510/AT1G55150/AT1G56410/AT1G60170/AT1G60200/... 84
00450 Selenocompound metabolism 13/2577 18/3449 0.722 0.967 -0.244 0.708 0.899 0.822 AT1G08490/AT1G19920/AT1G33320/AT1G64660/AT2G17420/AT2G41680/AT3G55400/AT3G57050/AT4G13780/AT4G35460/AT5G17920/AT5G20980/AT5G49810 13
00565 Ether lipid metabolism 13/2577 18/3449 0.722 0.967 -0.244 0.708 0.899 0.822 AT1G13560/AT1G55180/AT2G42010/AT2G45670/AT3G03530/AT3G03540/AT3G05630/AT3G15730/AT3G16785/AT3G48610/AT4G11840/AT4G11850/AT5G25370 13
04626 Plant-pathogen interaction 108/2577 148/3449 0.730 0.977 -0.499 0.727 0.912 0.834 AT1G01340/AT1G12220/AT1G17380/AT1G18210/AT1G19780/AT1G24620/AT1G32250/AT1G32640/AT1G35670/AT1G62820/AT1G64060/AT1G66400/AT1G66410/AT1G73630/AT1G74740/AT1G74950/AT1G76640/AT1G76650/AT1G80460/AT2G13790/... 108
00460 Cyanoamino acid metabolism 20/2577 28/3449 0.714 0.956 -0.402 0.739 0.915 0.837 AT1G22020/AT1G26560/AT1G36370/AT1G61820/AT1G69820/AT1G73050/AT2G44480/AT3G44300/AT3G44310/AT3G44320/AT3G47000/AT3G47050/AT4G13890/AT4G29210/AT4G32520/AT4G37930/AT4G39640/AT5G26780/AT5G42260/AT5G44640 20
04710 Circadian rhythm 17/2577 24/3449 0.708 0.948 -0.439 0.757 0.920 0.841 AT1G10230/AT1G20140/AT2G03160/AT2G03190/AT2G25700/AT3G21840/AT3G21850/AT3G21860/AT3G23340/AT3G25650/AT3G42830/AT3G60020/AT4G14340/AT4G34210/AT4G34470/AT5G20570/AT5G42190 17
00190 Oxidative phosphorylation 92/2577 127/3449 0.724 0.970 -0.601 0.762 0.920 0.841 AT1G01050/AT1G15120/AT1G16700/AT1G16780/AT1G17260/AT1G20260/AT1G22450/AT1G32710/AT1G49140/AT1G65290/AT1G75630/AT1G76030/AT1G78900/AT1G79010/AT1G80660/AT2G02050/AT2G07560/AT2G07671/AT2G07751/AT2G07687/... 92
00040 Pentose and glucuronate interconversions 42/2577 59/3449 0.712 0.953 -0.629 0.785 0.937 0.856 AT1G11590/AT1G23800/AT1G30350/AT1G44170/AT1G63290/AT1G67750/AT2G02720/AT2G47030/AT3G01270/AT3G03250/AT3G07010/AT3G15720/AT3G24230/AT3G27400/AT3G29090/AT3G29360/AT3G43270/AT3G48000/AT3G53190/AT3G54920/... 42
00562 Inositol phosphate metabolism 38/2577 54/3449 0.704 0.942 -0.741 0.817 0.963 0.880 AT1G10900/AT1G14520/AT1G21980/AT1G31190/AT1G49340/AT1G60490/AT1G60890/AT1G68000/AT2G14170/AT2G19800/AT2G21170/AT2G22240/AT2G26420/AT2G40116/AT2G41210/AT3G03530/AT3G03540/AT3G07960/AT3G09920/AT3G14270/... 38
00904 Diterpenoid biosynthesis 8/2577 12/3449 0.667 0.892 -0.643 0.837 0.975 0.891 AT1G05160/AT1G15550/AT1G79460/AT2G32440/AT2G34555/AT4G02780/AT5G25900/AT5G51810 8
00903 Limonene degradation 49/2577 70/3449 0.700 0.937 -0.917 0.854 0.983 0.899 AT1G11600/AT1G13100/AT1G13710/AT1G18270/AT1G23800/AT1G44170/AT2G30750/AT3G24360/AT3G26160/AT3G26170/AT3G26210/AT3G26220/AT3G26230/AT3G26270/AT3G26290/AT3G26300/AT3G26310/AT3G26320/AT3G44250/AT3G48000/... 49
00195 Photosynthesis 31/2577 46/3449 0.674 0.902 -1.151 0.904 1.000 0.914 AT1G03130/AT1G06680/AT1G08380/AT1G10960/AT1G14150/AT1G30380/AT1G30510/AT1G32550/AT1G44575/AT1G52230/AT1G60950/AT1G67740/AT1G79040/AT2G07707/AT2G27510/AT2G30570/AT2G30790/AT3G16140/AT3G50820/AT4G02770/... 31
03060 Protein export 31/2577 46/3449 0.674 0.902 -1.151 0.904 1.000 0.914 AT1G21650/AT1G23465/AT1G24490/AT1G29310/AT1G29960/AT1G48160/AT1G48900/AT1G52600/AT1G67650/AT1G67680/AT1G78720/AT1G79940/AT2G18710/AT2G28800/AT2G34250/AT2G39960/AT2G45770/AT2G46470/AT3G20920/AT3G24590/... 31
00920 Sulfur metabolism 22/2577 34/3449 0.647 0.866 -1.350 0.935 1.000 0.914 AT1G19920/AT1G33320/AT1G55880/AT2G14750/AT2G17640/AT2G43750/AT3G01910/AT3G03630/AT3G04940/AT3G13110/AT3G57050/AT3G59760/AT4G05090/AT4G14880/AT4G39940/AT5G04590/AT5G09290/AT5G28020/AT5G28030/AT5G56760/... 22
04145 Phagosome 41/2577 62/3449 0.661 0.885 -1.570 0.954 1.000 0.914 AT1G09210/AT1G20260/AT1G29310/AT1G32270/AT1G51740/AT1G60490/AT1G75630/AT1G76030/AT1G78720/AT1G78900/AT2G16510/AT2G18710/AT2G21410/AT2G25610/AT2G28520/AT2G34250/AT3G08560/AT3G14270/AT3G16100/AT3G28710/... 41
00360 Phenylalanine metabolism 61/2577 92/3449 0.663 0.887 -1.882 0.975 1.000 0.914 AT1G06570/AT1G24110/AT1G24735/AT1G30870/AT1G34510/AT1G44970/AT1G49570/AT1G62800/AT1G62940/AT1G65060/AT1G68850/AT1G71695/AT1G71920/AT1G74540/AT2G18140/AT2G18150/AT2G18980/AT2G24800/AT2G30970/AT2G34060/... 61
03020 RNA polymerase 18/2577 30/3449 0.600 0.803 -1.863 0.977 1.000 0.914 AT1G06790/AT1G11475/AT1G29940/AT2G04630/AT2G15430/AT2G29540/AT3G13940/AT3G22320/AT3G49000/AT3G52090/AT3G57660/AT4G07950/AT4G21710/AT4G35800/AT5G41010/AT5G45140/AT5G51940/AT5G60040 18
00906 Carotenoid biosynthesis 14/2577 24/3449 0.583 0.781 -1.853 0.977 1.000 0.914 AT1G06820/AT1G08550/AT1G30100/AT2G27150/AT2G29090/AT3G04870/AT3G14440/AT3G24220/AT3G53130/AT4G14210/AT4G19230/AT5G17230/AT5G57030/AT5G67030 14
00908 Zeatin biosynthesis 12/2577 22/3449 0.545 0.730 -2.184 0.989 1.000 0.914 AT1G67110/AT1G68460/AT2G19500/AT2G27760/AT2G36750/AT2G36800/AT3G19160/AT3G23630/AT5G19040/AT5G20040/AT5G38450/AT5G56970 12
00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis 42/2577 67/3449 0.627 0.839 -2.288 0.990 1.000 0.914 AT1G11600/AT1G13100/AT1G13710/AT1G24735/AT1G74540/AT2G30750/AT3G26160/AT3G26170/AT3G26210/AT3G26220/AT3G26230/AT3G26270/AT3G26290/AT3G26300/AT3G26310/AT3G26320/AT3G44250/AT3G52970/AT3G53290/AT4G13290/... 42
00940 Phenylpropanoid biosynthesis 70/2577 109/3449 0.642 0.860 -2.562 0.995 1.000 0.914 AT1G15950/AT1G24110/AT1G24735/AT1G26560/AT1G30870/AT1G34510/AT1G44970/AT1G49570/AT1G61820/AT1G62940/AT1G65060/AT1G67990/AT1G68850/AT1G71695/AT1G74540/AT2G18140/AT2G18150/AT2G18980/AT2G21730/AT2G21890/... 70
00941 Flavonoid biosynthesis 8/2577 19/3449 0.421 0.564 -3.279 0.999 1.000 0.914 AT1G24735/AT1G61720/AT1G74540/AT4G22870/AT4G22880/AT5G07990/AT5G08640/AT5G48930 8
03010 Ribosome 130/2577 220/3449 0.591 0.791 -5.511 1.000 1.000 0.914 AT1G09590/AT1G09690/AT1G12960/AT1G15250/AT1G17560/AT1G18540/AT1G22780/AT1G23410/AT1G26880/AT1G26910/AT1G33120/AT1G33140/AT1G35680/AT1G36240/AT1G41880/AT1G49400/AT1G52300/AT1G57660/AT1G57860/AT1G58380/... 130
04075 Plant hormone signal transduction 133/2577 232/3449 0.573 0.767 -6.309 1.000 1.000 0.914 AT1G03445/AT1G03970/AT1G04310/AT1G10940/AT1G17380/AT1G17550/AT1G19830/AT1G19850/AT1G22070/AT1G23160/AT1G27320/AT1G28130/AT1G32640/AT1G45249/AT1G48660/AT1G48670/AT1G49190/AT1G51950/AT1G52830/AT1G56150/... 133

表7.2 KEGG富集分析部分结果：
ID:KEGG通路标识符，前面省略"map"，比如“04120”代表“map04120”;
Description:KEGG通路的文字描述;
GeneRatio:该条目基因比例，分子是富集到这个KEGG通路上的基因的数目，分母是所有区域关联基因的数目;
BgRatio:背景比例，分母是物种全部有KEGG注释的基因的数目，分子是这些基因中注释到这个KEGG通路上面的基因的数目;
RichFactor​​:富集因子（Enrichment Factor）= GeneRatio / BgRatio;
​​FoldEnrichment​:富集倍数（Fold Enrichment）= (富集通路基因数 / 输入基因数) / (背景通路基因数 / 背景总基因数);
​​zScore​:标准化富集得分（基于超几何分布的 Z 值）;
pvalue:富集的p值;
p.adjust:使用BH校正之后的p值;
qvalue:q值,使用FDR校正之后的p值，q-value相比于p-value更加严格,表示p-value产生假阳性的概率;
geneID:富集到这个KEGG通路上面的具体的基因ID;
Count:富集到这个KEGG通路上面的基因的数目。



图7.4 区域关联基因KEGG气泡图。纵坐标是KEGG通路名称，横坐标是对应KEGG通路中检出的基因占背景基因的个数，颜色代表显著性，气泡大小代表该通路基因比例。



图7.5 区域关联基因KEGG条状图。纵坐标是KEGG通路名称，横坐标是出现在该通路的基因数，颜色代表显著性。






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