Question: Interpreting TCGA 450K data
1
gravatar for ChIP
5.9 years ago by
ChIP570
Netherlands
ChIP570 wrote:

Hello Everyone,

 

I was having a look at TCGA 450K data and I downloaded also the data at two levels, ie., level 2 and level3.

Level 2, looks like this:

Composite Element REF    Methylated_Intensity    Unmethylated_Intensity    Detection_P_value
cg00000029    2488.00579881129    2281.3142892634    0
cg00000108    8943.62421381116    336.745081332759    0
cg00000109    3827.0493383932    219.47270455192    0
cg00000165    263.820225926362    2355.4623873349    0
cg00000236    3733.92206994152    722.124674419151    0
cg00000289    1503.38837282518    277.513187258243    0
cg00000292    9650.668135454    1618.68980927383    0
cg00000321    5918.34421148769    4384.53097589033    0

 

while level 3, looks like this:

Composite Element REF    Beta_value    Gene_Symbol    Chromosome    Genomic_Coordinate
cg00000029    0.521668865344633    RBL2    16    53468112
cg00000108    NA    C3orf35    3    37459206
cg00000109    NA    FNDC3B    3    171916037
cg00000165    0.100722321673368        1    91194674
cg00000236    0.837944995677383    VDAC3    8    42263294
cg00000289    0.844172640712807    ACTN1    14    69341139
cg00000292    0.856363617411664    ATP2A1    16    28890100
cg00000321    0.574436174742582    SFRP1    8    41167802

Anyone, who has used this data can please tell me how I can Identify the regions/genes that are hyper and hypo-methylated.

Thank you

 

methylation tcga 450k • 4.2k views
ADD COMMENTlink modified 5.9 years ago by Sean Davis26k • written 5.9 years ago by ChIP570
0
gravatar for Sean Davis
5.9 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

What you have downloaded are per-sample files describing the methylation values at single CG sites.  Hyper- and hypo-methylation are "relative" terms, so you will need to define two (or more) groups and then look for differential methylation.  

 

ADD COMMENTlink written 5.9 years ago by Sean Davis26k

Hi Sean,

Thank you for your answer but I have another one for example say I have another group of values for second sample and I have to compare them and then identify regions that are hyper or hypo methylated? then which level of data shall I use (level2 or level 3) and how can I use it ? and secondly is it possible to use 3 Vs 13 samples to identify hyper and hypomethylated regions.

Thank ou

ADD REPLYlink written 5.9 years ago by ChIP570

You can use the level3 data, and compare the beta values between 2 or more groups. Logit transformation to M values will help with the statistical analysis.

You can also summarize multiple probes annotated to the same CpG island to a single value (e.g. mean) and compare the difference at the island level. Also M value will be helpful in comparison.

3 vs. 13 is OK.

ADD REPLYlink written 5.9 years ago by jianggl200040
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