生物信息学分析课件methylation

1、主要内容从GEO质控归一化差异甲基化位点差异甲基化区域注释数据甲基化Illumina Human Methylation 450K BeadChip可组近450,000个甲基化位点，具有单碱检测人全基的分辨率。全面覆盖了96%的CpG岛，并根据需求加入了CpG岛以外的CpG位点、人类干细胞非CpG甲基化位点、正常组织与肿瘤（多种）组织差异甲基化位点、编码区以外的CpG岛、miRNA启动子区域和GWAS疾病相关区域的位点，同时覆盖了Human点。Methylation27 BeadChip的90%的位的值A探针（非甲基化）的数目UB探针（甲基化）的数目M值或者m值m=log（ =M（M U 10

2、0）-1值反映了能够和给定被甲基化的序列匹配的寡核苷酸的比率，序列中的甲基化率M值可以消除探针不同而造成的影响2015/6/15数据1. GEO2. TCGA、EBI等其它质控质控归一化差异甲基化位点Iderceptfpvalqvalcg19229544-5.8198172499137.683047.18E-080.013840388cg137067693.1920619497427.7085051.09E-070.013840388ch.1.1262625R-16.609626056836.2767051.28E-070.013840388cg019723352.1445063985554.

3、8292211.94E-070.01571845cg19506433-0.652971394201.7085823.39E-070.02196957cg05945291-16.609626052652.5513598.51E-070.033324073cg21081097-6.2839646562621.4287148.71E-070.033324073cg080941352.3493027952547.0554339.22E-070.033324073cg25010146-5.2185579212449.9157499.97E-070.033324073热图差异甲基化区域chrstarten

4、dvalueareaclusterindexSt artindexE ndLcluster Lp.valuefwerchr125257191252582360.4341700338.68340066148661173211751203300chr11239720123979770.4238167838.05251888431573274030274048193700chr63193837231939112- 0.4346384127.38885300916398116387500chr6149805995149806732- 0.5585011816.143512994170492181364

5、0chr2209224225209225183- 0.6179528483.70771708611590073375733806800差异甲基化区域value-average smooth methylation difference within blockarea-block area estimate (abs(value) * length)cluster-id of cluster blockgroup within which block occursindexStart-index ofcluster in blockindexEnd-index of last cluster in blockL-number of clusters in blockclusterL-number of probes in blockp.value-permuion p.value based on difference conditioned on lengthfwer-family-wise error rate estimate based on difference conditioned on lengthp.valueArea-permu