Methylation scores from TCGA

Question

[Ron]

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.

Thanks,
Ron

Answer 1

[alolex]

Use the UCSC Table Browser to extract the coordinates of the promoter regions of interest (see this post), then query your text file for any rows that have coordinates within these regions.

Answer 2

[Charles Warden]

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).