Question: Microarray And Epigenomic Data For Same Cancer Cell Line?
1
gravatar for dirigible2012
6.1 years ago by
dirigible2012320
European Union
dirigible2012320 wrote:

I am doing a short project looking into the causes of misregulation of gene expression in cancer. I would like to compare epigenomic datasets with microarray expression datasets to see how much epigenetic dysregulation contributes to dysregulation of expression.

The problem is, I can't find a cancer dataset that contains both whole genome epigenetic data AND microarray expression data.

Does anybody have any ideas as to where I could find such a dataset, or how to go about looking?

(I'm aware it's only possible to get a subset of the epigenetic marks - I'd even settle for only methylation! :-)

Thank you, Stephanie

microarray cancer • 2.3k views
ADD COMMENTlink modified 6.1 years ago by dario.garvan460 • written 6.1 years ago by dirigible2012320

I don't think anybody does microarrays any more. You probably want RNASeq data instead.

ADD REPLYlink written 6.1 years ago by Emily_Ensembl20k

Good point, thanks. It's more finding the epigenomics data which is giving me trouble. I wonder if people simply aren't doing whole genomes.

ADD REPLYlink written 6.1 years ago by dirigible2012320
3
gravatar for lkmklsmn
6.1 years ago by
lkmklsmn920
United States
lkmklsmn920 wrote:

My best guess would be the The Cancer Genome Atlas (TCGA). https://tcga-data.nci.nih.gov/tcga/

ADD COMMENTlink written 6.1 years ago by lkmklsmn920
1

I agree, for example here: https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LAML&diseaseName=Acute%20Myeloid%20Leukemia you can see there is expression and mRNA expression for AML. YOu can go here: https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm?mode=ApplyFilter&showMatrix=true&diseaseType=LAML&tumorNormal=TN&tumorNormal=T&tumorNormal=NT and choose rows that have both.

ADD REPLYlink written 6.1 years ago by brentp23k

I clicked the second link you provided to download the data. I selected two RNAseq files which are TumorNormal pair.  SCreenshot of which files were selected can be seen here.

https://www.dropbox.com/s/u4xj9fr1mxii1my/Screen%20Shot%202014-09-18%20at%2021.35.22.png?dl=0

For each library selected, there are 6 files (gene expression level, isoform levels and so on) and altogether 12 files for two libraries.

Since this is TN pair, the gene expression measure from the result file represent for which RNA (tumor or normal). Am i understanding something wrong about TN pair ?

 

The selected file (small) can be downloaded from here
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/userCreatedArchives/fb8f00d7-a1b9-49df-86e1-e260e3b5bd80.tar

Any suggestions will be helpful.

ADD REPLYlink written 5.6 years ago by Chirag Nepal2.2k

Yes, TCGA has many such datasets.

ADD REPLYlink written 6.1 years ago by Neilfws48k

Just what I was looking for, thanks!

ADD REPLYlink written 6.1 years ago by dirigible2012320
0
gravatar for dario.garvan
6.1 years ago by
dario.garvan460
Australia
dario.garvan460 wrote:

There are histone methylation, DNA methylation, and gene expression datasets available for the prostate cancer cell line, LNCaP.

TCGA has a lot of biological replicates for each type of experiment, so it is better.

ADD COMMENTlink written 6.1 years ago by dario.garvan460
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