Is cBioportal and TCGA dabase is same?

[Rohail Jawed]

Hi,

This is jawed from pakistan. I want to know that cBioportal is a separate database or it is a subordinate of TCGA dabase. The data I have dowloaded is from cBioportal so should i have to give the web addess of cBioportal or TCGA database for citation? please suggest me.

Thanks.

[JJ Gao]

Hi Rohail,

cBioPortal contains TCGA data and a lot more other datasets, so it's not a subordinate of TCGA. When using cBioPortal for analysis, please cite our papers (https://www.cbioportal.org/faq#how-do-i-cite-the-cbioportal). If your analysis is based on particular studies in the cBioPortal, please cite these studies as well.

Thanks,

-JJ 

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[JJ Gao]

Hi Rohail,

Would you please let me know which study or studies you are looking at so that I can better answer your question?

Thanks,

-JJ

On Wed, Mar 16, 2022 at 12:57 AM Rohail Jawed <rohai...@gmail.com> wrote:

Hello Sir,

Thanks for your quick and kind reply. I want to confirm from you again that the data(clinical and expression) I have downloaded is only available on your cbioportal database not other databases like TCGA. I found that study on pubmed. I do not know why it is not available at TCGA database but available at your database, is it possible? please confirm.

Is cbioportal only a computational tool or can be used to download the cancer genomic data?

Thanks

[JJ Gao]

Hi Rohail,

Thanks for the info. This study is not a TCGA study and was curated directly from the publication. The mRNA data from the Supplementary Table 10: https://www.nature.com/articles/nature14664#Sec35

Best,

-JJ

On Thu, Mar 17, 2022 at 11:47 AM Rohail Jawed <rohai...@gmail.com> wrote:

Hello Sir,

Thanks for your response. I am working on the gene expression of small cell lung cancer. please see attached pictures. Among these four study only 1 study have expression data of 81 patients. This expression data is only available on the bioportal. please give me the original source of this data if possible. I do not find this data on any other database. Also, please assure me that can I  download this 81 patient mRNA expression data and use.

Thanks alot Sir.