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there! Could anyone help me with some biostatistical problems using cBioPortal.

We are looking for cell lines with upregulation of certain genes on cBioPortal. My supervisor is teaching me to use this website because I have no prior experience. She is using EXP >= 0.5 to define upregulation. Although I am of no bioinformatics background, my opinion is that 0.5SD away from the average is not strong enough to define an upregulation. I think it better to use EXP >= 2 or 1.5. I have discussed this with my supervisor but she insists using EXP >= 0.5.

Does anyone have any experience with this issue since I am still not convinced by what I was told. Thanks a lot!

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Well, I have worked with expression patterns. Unfortunately there is no clear cut or magical numbers for cutoffs . I agree with you that 0.5 is not stringent. However, to explore data usually one can parse it using lower cutoffs and later on you can rise the bar to see what happens.

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  • $\begingroup$ Many thanks Andrei! I also asked a friend of mine about this and she has similar opinions with yours. I will do queries with different criteria and compare the results! Thanks a lot! $\endgroup$ – Hubert. H. Chen Feb 21 '17 at 14:23

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