Download Isoform expression data from tcga
I am trying to identify the isoform of a gene that is overexpressed in cancer samples versus normal. Is there packages that would allow me to scan through all available cancer datasets on tcga and download isoform level expression data? Or do I need to start from raw rna seq data and map it to transcripts? Thank you
• 1,787 views
•
link
updated
by
t.fosk •
•
written
by
nourmahfel •
•
written
by
nourmahfel •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
TCGA raw RNA-Seq data
written by qwzhang0601
-
Isoform level TCGA RNA-seq Expression data
written by deepak18 •
-
Hypothesis testing for isoform level TCGA RNA-seq expression data
written by deepak18 •
-
TCGA - finding Normal and Tumor samples for matching protein and rna-seq samples
written by sid5427 •
-
Ttest on Rna-seq data
written by shivangi.agarwal800
-
How to compute survival analysis between LncRNA and one type cancer (i.e.Breast Cancer) based on TC…
written by ybling2008 •
-
In TCGA RNA-seq exon specific data, why not all the exons of a particular isoform have similar read…
written by ruhulmb •
-
How to get FASTQ files for diseased and receptive normal samples from TCGA database?
written by pbio
-
TCGA RNA-Seq, Expression levels in comparison with normal and connection with CNVs
written by thmourikis •
-
How To Map Isoform Ids Of Transcript To Entrez Ids ?
written by jack •
I have the same issue, did you got any response at the end? I still cannot find any isoform mRNA data, only miRNA is available.
Far as I know TCGA did not do transcript level expression as a standard analysis (see the list here --> https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ ).
You could check this database if you just need to look at some genes: http://www.tsvdb.com/ . GEPIA2 and CancerDEIso appear to be two other sites that seem to provide this analysis.
found some data here in case someone needs them in the future:
https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
Thanks!