Question: CCLE Gene Expression and RPPA data access
0
gravatar for Panagiout
18 months ago by
Panagiout0
Panagiout0 wrote:

We would really appreciate some input from the society, regarding the availability of CCLE data downloaded from https://portals.broadinstitute.org/ccle/about, and we really hope that this an appropriate place to get some additional information from research groups experienced in using such publicly available data.

We would like to use gene expression (microarray) and protein expression (RPPA) data from this portal, as input in a specific bioinformatic analysis we are conducting. We won't redistribute the data or use them for commercial purposes and of course we are going to provide the necessary acknowledgements. The terms and conditions highlight the fact that downloaded data should be used for internal research purposes. The question is do we need to ask for additional permission before using such data in our analysis and consequently in a potential publication?

Thank you !

ADD COMMENTlink modified 18 months ago by jared.andrews077.9k • written 18 months ago by Panagiout0

Dear @Panagiout, could you help me out a bit with RPPA data from CCLE?

Is this data raw, or processed? can it be directly used for comparison e.g. between cell lines, or does it need further processing? Who is/are the author(s) of the RPPA data results uploaded to the CCLE Database Portal? I cannot find any reference or literature regarding to this specific experiment. Do you know what does '_Caution' means in some of the probe ids?

Thank you!

ADD REPLYlink written 16 months ago by smadera0

I am extremely sorry for the delay. Here is the article about the next generation sequencing and the RPPA data.

https://www.nature.com/articles/s41586-019-1186-3

" The fitted curve is plotted with both the observed and fitted signal intensi-ties on the y axis and the log2 concentration of proteins on the x axis for diagnostic purposes. The protein concentrations of each set of slides were then normalized for protein loading. Correction factor was calculated by first median‐centring across samples of all antibody experiments and then median‐centring across antibodies for each sample. "

Based on this part of the article presented above, I believe that these are log2 normalized data, but for further information I suggest trying to contact them via the email in the CCLE portal (any new info on the matter is much appreciated).

Caution refers to the extend they managed to validate RPPA results by Western Blotting, in order to check the antibody performance. As far as I remember, they validate RPPA results by correlating them to Western Blot results, but I might be mistaken about the procedure. Check the MD Anderson RPPA facility site

https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core/antibody-information-and-protocols.html

Cheers !

Στις Δευ, 8 Ιουλ 2019 στις 9:02 μ.μ., ο/η smadera on Biostar < mailer@biostars.org> έγραψε:

ADD REPLYlink modified 16 months ago • written 16 months ago by Panagiout0
1
gravatar for jared.andrews07
18 months ago by
jared.andrews077.9k
Memphis, TN
jared.andrews077.9k wrote:

It looks like you're fine, assuming you give proper acknowledgments and don't reveal any identifying patient info:

Data Protection: You agree that You shall not analyze or make any use of the Data in such a way that has the potential to: (i) lead to the identification of any Data Subject; or (ii) compromise the anonymity of any Data Subject in any way.

You agree to take all reasonable security precautions to keep the Data confidential, such precautions to be no less onerous than those applied in respect of your own confidential information.

Publications: You agree to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the Data, and the role of the Broad in its distribution. You agree to use the acknowledgement wording provided for the relevant Data in its publication. You will also declare in any such work that those who carried out the original analysis and collection of the Data bear no responsibility for the further analysis or interpretation of it.

Then again, I'm not a lawyer, so don't take this as legal advice.

ADD COMMENTlink written 18 months ago by jared.andrews077.9k

Greatly appreciated, thank you ! Won't take it as legal advice for sure, I'm just asking for some experience-based feedback in similar situations.

ADD REPLYlink written 18 months ago by Panagiout0
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