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=== Correlation of high density CpG regions in 450K array=== <gallery widths=400px heights=400px> File:Density.CorrelationDifferenceBetweenCancerNormal.jpg|Figure 2. Density plot for the correlation of high density CpG regions in 450K array between cancer and normals File:CorrelationDifferenceBetweenCancerNormal.jpg|Figure 3. Comparison of the correlation for the high density CpG regions in 450K array between cancer and normals </gallery> *It is very interesting result: 1) cancer have two peak 2) cancer have more higher correction regions Comparing the correlation of HDR, we could find the similarity of the correlation between cancer and normal were interrupted. the cancer tissues had more high correlated HDRs than the normal tissues. What's more, obviously, there is only one peak in the density plot of correlations in the normal tissues while there is an extra peaks in the cancer tissues. Based on the Figure 3, I think, the region whose average correlation is large than 0.5 (cut-off) can be defined as methylation block. However, the performance of cut-off of 0.4, 0.5, 0.6 were analysis in the following section. The result can be found in the below figure. Although the number of the conservative regions were quite different (left), the relative proportion of the conservative regions were almost same (right). I don't know how to set a unique threshold to define methylation block, In additional, there is no such unique threshold to define LD in population genetics, therefore, I think an arbitrary cut-off should be set here. <gallery widths=400px heights=200px> File:Picture4ConservationFragtmentin450kdataset.png| Figure 4A. Conversation Methylation Block Screening among 11 TCGA Normal dataset. File:ConservationFragtmentin450kdataset.Cancer.jpg| Figure 4B. Conversation Methylation Block Screening among 11 TCGA Cancer dataset. </gallery> As the obove figure showed, different cut-off of the definition of methythylation block were almost similar when average correlation is larger than 0.4, [[2015-7-10-001-code]] *2421 Common methylation blocks in TCGA normal datset: [[File:Conservative.methylation.block.0.6.bed.txt]] *155 Shared methylation blocks in 11 normal samples: [[File:Conservative.methylation.block.C11.0.6.bed.txt]] Similarly, we can get the shared high correlated HDRs in cancer samples [[2015-7-10-002-code]] Here, I want to show that these 2421 regions were no specially selected in 11 cancers. Suppose, these 2421 regions were derived from a same population, then the frequency of each regions occurred in 11 samples would have binomial distribution. therefore, we test each regions one by one and no any one of the regions significantly deviate from the theoretical [[distribution]]. In this analysis, P=0.399 {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''Observe''' | align="center" style="background:#f0f0f0;"|'''Expectation''' |- | 1||602||968.4 |- | 2||402||387.36 |- | 3||255||154.944 |- | 4||215||61.9776 |- | 5||140||24.79104 |- | 6||126||9.916416 |- | 7||138||3.9665664 |- | 8||95||1.5866266 |- | 9||198||0.6346506 |- | 10||100||0.2538602 |- | 11||150||0.1015441 |- | |}
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