Entering edit mode
3.0 years ago
nourmahfel
▴
10
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
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!