I am trying to analyze TCGA data for breast cancer but I cannot do. Recently one study published in oncogene [Oncogene (2016) 35, 6120–6131]. In this paper they use TCGA data of lung adenocarcinoma for studying GPC5 gene function in cancer.
They mention in the paper that "We used the TCGA database
to analyze the correlation between GPC5 and all other genes in
patients with lung adenocarcinoma. We found that 12 830 gene
expression levels have significant correlations with GPC5 (Po0.05)
(data not shown)." page no-6124.
I want to get this kind of correlated genes for another gene but I couldn't.
Can anybody help me how to get this data from TCGA database?
Hi,
you can access and download most data by the TCGA website. For some data you have to ask for permission (if I remember correctly):
https://cancergenome.nih.gov/
Moreover several websites enable "simple" analyses using TCGA data:
http://www.cbioportal.org/index.do
http://kmplot.com/analysis/index.php?p=service&cancer=breast
and here you have an overview over available tools
https://omictools.com/tcga-data-access-category
Regards,
Norman
...it seems that the TCGA portal is closed and data are accessible in the GDC portal
https://gdc.cancer.gov/
Hello
See links here
Good Luck
https://www.youtube.com/watch?v=2Bc8TOkwCpc
https://docs.gdc.cancer.gov/Data_Portal/PDF/Data_Portal_UG.pdf
Hi
I think this paper will help you to get more information from TCGA.
Thanks
Dear Yuanzhi Jim Lu,
the article you sent saved me! It is very useful, thank you so much!!
Hi, Saleh Alkarim and Yuanzhi Jim Lu, I am also tring to learn how to use TCGA, thanks a lot for your help~~
To create PI account in TCGA, comons user with an SO, AA or BO role is needed.
How to create commons account ?
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