I need to compare a gene's expression between tumor site and matched normal tissue from TCGA database. I've tried using Firehose to search differential expression of the gene among different types of cancers. The problem is that the amount of tumor samples is not equal to the amount of normal samples. But I need to compare matched tumors and normal tissues. Is there any tools to do that?
I think that the best way to make a comparison beteween two genes is by sequencing them. Regarding your question, you should sequence your tumor gene and compare it with the matched normal (that is already sequenced). This will give you the differences in tcga sequence.
But if you want to know the expression differences you might need to do a plasmid construct and study the results of its expression.
You will have to study also the metilation of both genes and the metilation of some areas that may be far from the transcrition portion of the gene. These areas may be related with the bonding of co-promoters and enhancers.
In some types of cancers you may find that there is no mutation of the gene but that gene is silenced by metilation of promoter and co-promoter areas. This is usually found in anti-oncogenes as p53 and PTEN.
@Yijun Nice website! Do you know how to use this website to visualize RNA level difference of a gene between tumor and normal samples?
http://www.cbioportal.org/
Try above link which is fantastic to compare gene expression between tumor and matched normal tissue
A tool that directly does what you asked, I don t think exist yet.
Use this R package to download the already pre-processed data from GDC (TCGA) repository and perform all the analysis you want. Use the patients id to find matching tumor and normal samples for each patient.
link to the R package:
https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html
If you now R, will be really simple to do what you asked :)
If you know a little bit of coding in R, try to download whatever database you are interested in (TCGA, Pan-Cancer-Atlas, GDC...), by using the package UCSCXenaTools, and then perform gene expression comparison between tumor and normal tissues. You can also use UCSC Xena, as recommended by Yijun Tian.
Package: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
GEPIA has a nice user interface to select cancer subtypes "subtype of interest for further analysis, or compare different subtypes for expression and survival."
http://gepia.cancer-pku.cn/index.html
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