TCGA Dataset of cancer study

Question

[vrrani]

1. Can gene expression data of Broad Institute HT-HG-U133A platform, be called as transcriptome data?
2. Can Methylation data of JHU-USC-Illumina-DNA-Methylation platform be called as Epigenome data?

[lakhujanivijay]

Hello vrrani

you are not supposed to post the same stuff multiple times as you did for this post here. I have closed that post.

Additionally, please take some time to elaborate on your question and provide additional details, possibly links to the stuff you are referencing to. This will help increase the chances for you to get an answer

Thanks

[vrrani]

Thank you.

In the one of the article I am reading (Integration of Gene Expression Data and Methylation Reveals Genetic Networks for Glioblastoma), they had alternatively used the term 'transcriptome data' for 'gene expression data' and 'Epigenome data' for 'Methylation data'.

I am new to biology domain, wanted to know in whcih context, such way of expression is valid.

Answer 1

[Kevin Blighe]

The answer to both of your questions is 'yes'.

The HT-HG-U133A is a microarray, which profiles the transcriptome in a biased / supervised fashion. What do I mean by biased / supervised? - I refer to the fact that the probes on the microarray are designed to target already known mRNAs. Microarrays cannot [easily] detect novel mRNA species (but RNA-seq can).

Methylation is related to the epigenome because the process of methylation involves the modificaion of DNA via the addition/removal of methyl chemical groups.

That's it, simply explained.

Kevin