Question: Methylation scores from TCGA
gravatar for Ron
5.1 years ago by
United States
Ron1000 wrote:


Hi all,

I am analyzing methylation scores for TCGA samples.But I want to only look at regions around the promoter region like 4 kb and not all the regions in a gene.

Composite Element REF Beta_value Gene_Symbol Chromosome Genomic_Coordinate
cg00000029 0.118076889 RBL2 16 53468112
cg00000108 NA C3orf35 3 37459206
cg00000109 NA FNDC3B 3 171916037
cg00000165 0.935985622   1 91194674
cg00000236 0.914543649 VDAC3 8 42263294
cg00000289 0.804443532 ACTN1 14 69341139
cg00000292 0.467988802 ATP2A1 16 28890100
cg00000321 0.436909485 SFRP1 8 41167802
cg00000363 0.082935365   1 230560793
cg00000622 0.012932961 NIPA2 15 23034447
cg00000658 0.887374126 MAN1B1 9 139997924
cg00000714 0.083851745 TSEN34 19 54695678
cg00000721 0.943942042 LRRC16A 6 25282779
cg00000734 0.057197822 CNBP 3 128902377
cg00000769 0.01915944 DDX55 12 124086477
cg00000807 NA KLHL29 2 23913414
cg00000884 NA TLR2 4 154609857
cg00000905 0.062501621 FAM81A 15 59785306
cg00000924 0.921750637 KCNQ1;KCNQ1OT1 11 2720463



How can I only chose the regions around the promoter based on the above information.The above is just a subset of the data from a sample. 



methylation next-gen gene • 1.6k views
ADD COMMENTlink modified 5.1 years ago by Charles Warden7.8k • written 5.1 years ago by Ron1000
gravatar for alolex
5.1 years ago by
United States
alolex910 wrote:

Use the UCSC Table Browser to extract the coordinates of the promoter regions of interest (see this post A: How To Get Promoter Sequences For Human Genes? ), then query your text file for any rows that have coordinates within these regions.

ADD COMMENTlink written 5.1 years ago by alolex910
gravatar for Charles Warden
5.1 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

If you are satisfied with TSS500 or TSS1500, then the array already has annotations for those promoter regions.  You can download the .bpm file to get those annotations, or use any of the strategies from this post:

How To Annotate Methylation 450K?

Or, if you are interesting in differentially methylated regions, IMA will strategy results based upon annotations, including the TSS annotations (once you get the data in a format that works as input to the IMA functions).

ADD COMMENTlink written 5.1 years ago by Charles Warden7.8k
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