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Alice:Whole Genome Bisulfite Sequencing Lab Notes/WGBS
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==correlation between CpG island shore methylation and gene expression levels== *method #1: #download the gene annotation file from UCSC #use "bedtools closest" command to find the closest CpG island shore location of a given gene #trim down the output file using following criteria: ##genes on + strand with end of CpG shore- beginning of gene < 0; ##genes on - strand with end of gene - beginning of CpG shore > 0 #now we have created all the known CpG island shore location for a list of genes #compile a list of genes that are differentially expressed between SCNT-ESC and iPSC or iPSC and ESC (look for literature) #find the methylation level of the CpG shore for these genes *how to calculate the p-value? **split CpG island shore methylation into 2 groups: differentially methylated and non-differential methylation **find genes that are differentially expressed in the above two groups **chi-square test for relationship between CpG shore methylation and gene expression *Discussion: this method isn't going to work because we have only observed enrichment of DMR at CpG shore, it is not a very strong signal such that high # of DMRs are all located at the shore, so the observations we can fit into the above groups would be very small. So we should try to find another way to look for correlation between the groups. *method #2: #find DMS that is located at CpG island shore using bedtools (found 12 out of 111 total DMS) #extend the CpG shore region we have identified from previous step by 2k in both direction (total length of the region is now 6k) #extract the methylation frequency at these locations #find the gene expression level of these genes #do correlation test between the methylation and gene expression level #the genes below are the three candidates identified by above method, but the results weren't informative to make any conclusion {| {{table}} | align="center" style="background:#f0f0f0;"|'''GENE*Transcript''' |- | HSPA2*NM_021979 |- | ZNF212*NM_012256 |- | SIM1*NM_005068 |}
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