Use of TCGA database to get information on protein Expression

Question

[som.mukherjee.bio]

Is there any particular GUI based tool or any standard methodology which would enable me to visualize the differential expression levels of a particular protein in different stages of breast cancer?" I am totally naive in this field and still exploring the possible methods and ways.

Answer 1

[EagleEye]

You can find the expression dataset for TCGA which covers almost all protein coding genes in 'synapse' project.

https://www.synapse.org/#!Synapse:syn362400/files/

A: MiTranscriptome data access (discussed)

or these might be helpful,

http://www.compgenome.org/TCGA-Assembler/

http://bioinfo-out.curie.fr/ittaca/

Answer 2

[Lluís R.]

First of all you need to have such information about expression levels in different stages of breast cancer. As far as I know, there isn't a clear variable of cancer progression associated with TCGA dataset, at most you have a ajcc_stage indicator (which I don't know much). You may have two samples of the same person, which is not easily traced to when were these samples extracted. But other may have more information about the project.

I don't know such a GUI tool to know the expression at different stages of cancer. But with R and Bioconductor you could build that yourself.

Answer 3

[igor]

cBioPortal?

http://www.cbioportal.org/study.do?cancer_study_id=brca_tcga_pub2015#summary