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Question on Phosphopath #1

Open ucsdwxu opened 5 years ago

ucsdwxu commented 5 years ago

Hi, I have a question regarding the "dataset.phos" file here. For this data file, shall I just include those fold change of either upregulated or downregulated for 2-fold and in the exactly same format as from the example from Github? If it is a single-time point experiment only, how does Phosphopath know which are upregulated and which are downregulated?

Thank you very much for your help in advance.

Best regards, Weijun

phornbeck commented 5 years ago

Hi Weijun,

I believe that you want to contact Dr. Maarten Altelaar at 'm.altelaar@uu.nl' who published the PhosphoPath paper: "PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks. J Proteome Res. 2015 14:4332-41". I am CCing Maarten here, as it is possible that you are referring to a dataset that PhosphoPath derived from our website.

Regards, Peter

Peter Hornbeck, Ph.D. Senior Scientist & PI PhosphoSitePlus Cell Signaling Technology 3 Trask Lane Danvers MA 01923 http://www.phosphosite.org/ office: 978 8672368 cell: 978 7664970 Skype: cst_phornbeck

On Sat, Feb 23, 2019 at 12:50 PM ucsdwxu notifications@github.com wrote:

Hi, I have a question regarding the "dataset.phos" file here. For this data file, shall I just include those fold change of either upregulated or downregulated for 2-fold and in the exactly same format as from the example from Github? If it is a single-time point experiment only, how does Phosphopath know which are upregulated and which are downregulated?

Thank you very much for your help in advance.

Best regards, Weijun

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ucsdwxu commented 5 years ago

Dear Peter,

Thank you for your information. I will contact Dr Maarten Altelaar for advice.

Best, Weijun

phornbeck commented 5 years ago

You are welcome, and good luck in your research!

Peter

Peter Hornbeck, Ph.D. Senior Scientist & PI PhosphoSitePlus Cell Signaling Technology 3 Trask Lane Danvers MA 01923 http://www.phosphosite.org/ office: 978 8672368 cell: 978 7664970 Skype: cst_phornbeck

On Sat, Feb 23, 2019 at 1:38 PM ucsdwxu notifications@github.com wrote:

Dear Peter,

Thank you for your information. I will contact Dr Maarten Altelaar for advice.

Best, Weijun

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/linseyr/PhosphoPath/issues/1#issuecomment-466676944, or mute the thread https://github.com/notifications/unsubscribe-auth/ANnhD6i9hkGA0_WoOfehbf8ie5b0sJ1Vks5vQYq7gaJpZM4bOEWu .

-- This message contains information which may be confidential and/or protected by attorney-client privilege.  Unless you are the addressee, you may not use, copy or disclose to anyone this message or any information contained in this message.  If you have received this message in error, please send me an email and delete this message.   Thank you.