Cancer Genomics (Part 3): Easy guide to access RNA sequencing data of cancer (Example: Cbioportal)

[@mustaphaelzeini8722]

you have no idea how much this video helped me. keep up the good work. thank you !!

[@FarhanHaqj]

pleasure

[@suryagubbi756]

Hi Farhan, I had a question.... How could we find the fold change of expression for genes of all patient samples for a particular cancer using the Cbioportal? What I mean by fold change is the difference in expression level between a primary tumour sample and normal tissue sample of a particular gene. That way we can find out if the genes are being over expressed or under expressed. Thank you for the wonderful video!

[@FarhanHaqj]

Cbioportal doesnot provide foldchange or DEGs. It gives z-score kr normalised expression values

[@suryagubbi756]

@@FarhanHaqj Is there any way to figure out if a gene is being over or under expressed? Could the z score and normalised expression values indicate an over expression, under expression or normal values?

[@FarhanHaqj]

@@suryagubbi756 yes as this cbioportal has set a threshold of 2 as upregulatef and - 2 as downregulated

[@suryagubbi756]

@@FarhanHaqj Noted. Thank you so much for taking the time to reply, and thank you for the videos.

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[@ImranKhan-ov1ce]

Good Work. I hope actual research is going well?

[@andyderek3021]

Please, can you send me the link to your video for TCGA database dataset tutorial?

[@FarhanHaqj]

Search bioportal

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Hayatullah Fa19-rbm-013

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Hi Farhan,

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