Proteome annotation tuto with ProteoRE

[combesf]

pull request by Flo tu be pushed on the GTN

[combesf]

I updated the CONTRIBUTORS.yaml file

[combesf]

Hello, Thanks @shiltemann for your comments. I update according to your suggestions !

thanks @bebatut for your email

[shiltemann]

Thanks @combesf!

Can I make one small request: could you in the future please refresh your browser window right before making any changes? Otherwise changes others may have made to the file since you last refreshed will be undone again. Thanks!

[combesf]

update done, except for the zenodo links format caus it was already ih this format (@bebatut ?) Thanks a lot

[combesf]

All done (I really think)

[combesf]

Hello @shiltemann @bebatut Just a little ping in case you have time .. I hoped this could be online for the GCC conference next week .. Thanks a lot for your help,
Florence.

[shiltemann]

Hi @combesf thanks for letting us know this is for GCC, we have a lot of open pull requests to review, but will do our best to get around to everybody on time for the conference

[combesf]

hello @shiltemann do you think the tuto can be online soon ? Thanks a lot, Florence.

[foellmelanie]

Hi @combesf

I can review it today.

Best, Melanie

[foellmelanie]

Dear @combesf

I did the tutorial and enjoyed it a lot. Thank you for this nice contribution :)

I have a few suggestions for improving the tutorial. It would be very nice if you could add those.

• Images: To keep the image folder organized, it would be great if you could name the png files with the tutorial name as a suffix and then the image name or add a new folder as done for the "biomarker-selection" tutorial.

• It would be nice if you could add a small description of the training dataset/experimental design e.g. how was the EBC collected, what was the aim of the EBC studies, what was studied, healthy or diseased humans or both, how many samples, what was the technical control, how was the txt file for the training generated? A few sentences are probably enough but it helps the user to understand the big picture without having to read the publication.

• please add citation and maybe also link to for HPA

• (first) ID converter: output of Build tissue-specific expression dataset tool - wrong tool name?, the input file should be from: Filter by keywords and/or numerical value

• Introduce abbreviation TPM

• Hands-on: Check for proteins highly expressed in salivary glands: Suggestion: Add an additional step with the "Select lines that match an expression" tool, select for lines matching "salivary gland" - especially for large datasets that helps to visualize the presence of salivary gland proteins. For me this returns a list of 12 proteins (including the 8 proteins that are described in the training) - probably HPA annotation changes over time? Then a comment that slight differences might be expected due to updates in HPA.

• GO enrichment: I did not get EBO plots: Warning: No Go terms enriched (EGO) found - as Reactome looks similar as in the training I assume I did something wrong here or the 5 removed proteins from the HPA steps made a big difference here. Maybe at some point you have time to look into this...

• maybe you can add two sentences on what to do with the Reactome outcome

• Please use meaningful names for all three input files in the Venn Diagram tool

• two typos: the outpu file; that aims ti provide

Thanks again for this wonderful tutorial :) Melanie

[combesf]

Dear @foellmelanie I tried to answer most of your requests / suggestions and hope you will be ok with this version Thanks Florence.

[foellmelanie]

Dear @combesf

thanks a lot for improving the training :)

Before approving it I have a last request, please have a look at my suggestion, I think there was the wrong tool name in the hands on section (1st ID converter tool)?

Cheers, Melanie

[combesf]

Dear @foellmelanie you were right. I just accept your suggestion directly, I hope it is ok cheers and thanks a lot Florence.

[shiltemann]

Hi @combesf I will add a few last changes too. If you want to make any more updates after I (or others) have added changes here, please always make sure to first get the latest version of the files before updating and uploading new ones. Thanks again!

[combesf]

dear @shiltemann I reload pages to be sure to have the latest version. If it is not the case, it is that I do something wrong but I don't know what. @shiltemann @bebatut I created a new zenodo ref with the 3 datasets , and commit it in the md file. hope this is ok now !

[shiltemann]

@combesf no worries, and thanks for the Zenodo link!

[shiltemann]

Hi @combesf the tutorial looks great, thanks :) I made some final tweaks and added some examples for the missing key_points, but I am no expert here, so maybe you can just check them and let me know if you would like to change or add any?

Also, it is always nice to add question boxes inbetween steps so learners can check if they have understood the important points of the analysis, so if you can think of any nice questions that would be great (but we can add those later too)

@foellmelanie maybe you could also have a final look and then feel free to merge whenever you're happy with it :)

[combesf]

@shiltemann @foellmelanie it is ok like this for me, thanks a lot

[shiltemann]

:tada: