Dear everyone,
I'm working on bio-informatics. And my current project is to analyze public data from TCGA and GEO to find novel genes' relation to diagnosis or prognosis of cancer. The special feature of TCGA data is the enclosing clinical data, which we can use for further analysis.
I'm just want to know that is there any platform or source of public data like TCGA or GEO? Because sometimes I need to validate the data. But I can find another source for validation, and I have no available clinical data of the interest problem in my hospital.
Thank you very much for reading and sharing experience!!!
Hi,
A nice platform to explore public datasets such as TCGA, ENCODE, ROADMAP, GEO, and IHEC is the WashU Epigenome Browser, where you can access a broad range of transcription and epigenetic datasets, ranging from RNA-seq to WGBS, ChIP-seq, among others. Wash U harbors different datasets for hg19 and hg38 genomes, therefore I suggest that you explore both options.
I hope you find it useful.
Regards,
link: http://epigenomegateway.wustl.edu/browser/
You could use Human protein atlas for cross validation of the data
Shama Prasada Kabekkodu Andrés Hernández Oliveras I want to have genetic/epigenetic information enclosed with clinical information, because I need to predict the diagnostic or prognostic value. Except for TCGA, is there any other source like that?
Another option could be cBioportal ( https://www.cbioportal.org/ ), where you can access to genomic, epigenomic, and clinical data of several cancer datasets.
Regards,
Just go through cBIoPortal and UCSC XENA browser. you will get your queries solved. It will require a few days to learn but you may get the most out of it .
You can follow our publication, where we have utilized multiple tools to analyze TCGA data of breast cancer
Article Expression pattern, regulation, and clinical significance of...
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