histone marks in my methylation data

Question

[Pin.Bioinf]

Hello,

I want to check if there is preservation of methylation in the H3K36me3 marks in my data. Are there coordinates available of H3K36me3 marks? or how do people do histone analysis? my data is methylation and expression.

Could I check wether H3K36me3 is associated to genes and check for the methylation in those genes? Could I find H3K36me3 coordinates and check for methylation in that region?

Thank you

[Devon Ryan]

What cell type are you using? In general it's convenient to download called peaks from ENCODE or DEEP or something for your cell type (or get something from GEO if applicable).

[Pin.Bioinf]

Its HepG2,

Once i have the downloaded called peaks what will i have? What steps do i have to follow?

[Devon Ryan]

What do you think?

[Pin.Bioinf]

I mean, what does called peaks data look like? Maybe a bam file?

[Pin.Bioinf]

I downloaded the called peaks in .bed format from https://www.encodeproject.org/experiments/ENCSR000AMB/

and this is what it looks like:

chr3    93470303    93470914    Peak_1  1000    .   5.84259 49.47162    39.98125    290
chr14   39090432    39091388    Peak_2  993 .   18.22485    49.18372    39.98125    327
chr2    215386242   215389220   Peak_3  939 .   21.04010    46.53011    38.48376    617
chr14   34596605    34597782    Peak_4  926 .   20.32126    45.95149    38.13322    573
chr14   23077648    23080776    Peak_5  914 .   18.24496    45.36000    37.65496    1265
chr14   23060214    23061455    Peak_6  895 .   18.60350    44.47067    36.88879    846
chr6    166946796   166948173   Peak_7  851 .   20.08308    42.35030    35.13869    988
chr14   31128394    31131530    Peak_8  845 .   17.19519    42.08554    34.97175    839
chr6    7566644 7572177 Peak_9  830 .   19.81797    41.31627    34.24750    2611
chr20   47297215    47299648    Peak_10 809 .   17.89050    40.39828    33.48541    1595
chr16   8896393 8897657 Peak_11 809 .   18.26622    40.35860    33.45707    445

Are those coordinates for histone marks?

[Devon Ryan]

Yes, those are the regions where the modification is likely present.

[Pin.Bioinf]

Thank you!!

2018-04-25 11:56 GMT+02:00 Devon Ryan on Biostar [e-mail]: