How to include proteins that were not linked in the network

[AnnaKuchmiy]

Dear, in my list of proteins some of them are not linked in the network but still belong to one process, how can I format those proteins in the table for the upload?
Many thanks in advance!

[PavlopoulosLab]

Help Pages>Input File *Troubleshooting:*Nodes referenced in the annotation file must comply with nodes referenced in the network file. If a node in the annotation does not appear in the network file, NORMA won't be able to process the files and produce a proper visualization. To address this problem, we have implemented an R script which accepts a network file and an annotation file as inputs and generates a corrected annotation output file. In this output file, node names in annotations which do not appear in the network file are discarded. Notably, node names in both files must not contain any commas (,). Download R script here <http://bib.fleming.gr:3838/NORMA/session/5f177c032106beb3444b0f88185f64de/download/R_script?w=> - Install R / Rstudio - Open the file with Rstudio - Run the file - The output will be written in a new file named 'annotations_cleaned.txt'.

[AnnaKuchmiy]

Thank you for the quick reply, I guess I need to explain the problem a little bit more. I've generated a network file from this STRING analysis

I would like the nodes that were not linked to the network, but still making the functional group to appear (e.g. CEACAM1,ADD3,TTN) to be added in the network upload in NORMA.
Source Target
ADD3 ADD3 (something like this)
I was wondering whether this might be possible?
Many thanks,
Anna

[PavlopoulosLab]

We see the problem. Self-loops (ADD3 ADD3) are discarded so they will not even appear on the network Unfortunately we do not address this case in this version but this is certainly something that needs to be fixed.

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On Sun, Jan 17, 2021 at 6:56 PM AnnaKuchmiy ***@***.***> wrote: Thank you for the quick reply, I guess I need to explain the problem a little bit more. I've generated a network file from this STRING analysis [image: image] <https://user-images.githubusercontent.com/15571241/104849790-ed7ec880-58eb-11eb-81d8-04a489376f0d.png> I would like the nodes that were not linked to the network, but still making the functional group to appear (e.g. CEACAM1,ADD3,TTN) to be added in the network upload in NORMA. Source Target ADD3 ADD3 (something like this) I was wondering whether this might be possible? Many thanks, Anna — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOVBFDV572TMQGZRRSPHRULS2MJDPANCNFSM4WGG64SA> .

[AnnaKuchmiy]

Thank you very much for your consideration! I temporarily solved the problem by adding fake nodes (ADD3-FAKE1) and then removing them in HTML.
Best wishes,
Anna