Visualization of a gene expression data

Question

[evgenydeforzh]

Hi, guys A guy with no experience wants to find and visualize all isoforms of the gene of interest expressed in Lower Grade Glioma and Glioblastoma. I downloaded

GBMLGG.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data.Level_3.2016012800

assuming that I can get normalized isoforms from this file. The question is what should I do next to visualize them in Encode? Evgeny

[GenoMax]

Please change the title of this question to something more concise. It is messing up formatting of the title. You can find all isoforms of the gene at Ensembl, UCSC or Encode. I don't know if analysis at ENCODE was done at isoform level.

[evgenydeforzh]

Thanks, but I need to visualize isoforms expressed in Lower Grade Glioma and Glioblastoma, Encode and Ensemble shows all the transcripts ever annotated for every gene .

[jared.andrews07]

What do you mean by "visualize them in Encode"? Can you post a few lines so we can see what format the file is in? What is your purpose and what do you want to show?

[GenoMax]

OP wants to see which isoforms are specific to Glioblastoma.

evgenydeforzh : You would need to have something (a normal set) to compare the genes with to get relative information. Have you looked at TCGA glioblastoma publications if this analysis has already been done?